diff --git a/synapse/config/_base.py b/synapse/config/_base.py
index 20778973d5..8757416a60 100644
--- a/synapse/config/_base.py
+++ b/synapse/config/_base.py
@@ -136,11 +136,6 @@ class Config(object):
         with open(file_path) as file_stream:
             return file_stream.read()
 
-    @staticmethod
-    def read_config_file(file_path):
-        with open(file_path) as file_stream:
-            return yaml.safe_load(file_stream)
-
     def invoke_all(self, name, *args, **kargs):
         results = []
         for cls in type(self).mro():
@@ -158,9 +153,8 @@ class Config(object):
     ):
         """Build a default configuration file
 
-        This is used both when the user explicitly asks us to generate a config file
-        (eg with --generate_config), and before loading the config at runtime (to give
-        a base which the config files override)
+        This is used when the user explicitly asks us to generate a config file
+        (eg with --generate_config).
 
         Args:
             config_dir_path (str): The path where the config files are kept. Used to
@@ -182,10 +176,10 @@ class Config(object):
         Returns:
             str: the yaml config file
         """
-        default_config = "\n\n".join(
+        return "\n\n".join(
             dedent(conf)
             for conf in self.invoke_all(
-                "default_config",
+                "generate_config_section",
                 config_dir_path=config_dir_path,
                 data_dir_path=data_dir_path,
                 server_name=server_name,
@@ -194,8 +188,6 @@ class Config(object):
             )
         )
 
-        return default_config
-
     @classmethod
     def load_config(cls, description, argv):
         """Parse the commandline and config files
@@ -240,9 +232,7 @@ class Config(object):
         config_dir_path = os.path.abspath(config_dir_path)
         data_dir_path = os.getcwd()
 
-        config_dict = obj.read_config_files(
-            config_files, config_dir_path=config_dir_path, data_dir_path=data_dir_path
-        )
+        config_dict = read_config_files(config_files)
         obj.parse_config_dict(
             config_dict, config_dir_path=config_dir_path, data_dir_path=data_dir_path
         )
@@ -385,10 +375,7 @@ class Config(object):
         obj.invoke_all("add_arguments", parser)
         args = parser.parse_args(remaining_args)
 
-        config_dict = obj.read_config_files(
-            config_files, config_dir_path=config_dir_path, data_dir_path=data_dir_path
-        )
-
+        config_dict = read_config_files(config_files)
         if generate_missing_configs:
             obj.generate_missing_files(config_dict, config_dir_path)
             return None
@@ -400,53 +387,6 @@ class Config(object):
 
         return obj
 
-    def read_config_files(self, config_files, config_dir_path, data_dir_path):
-        """Read the config files into a dict
-
-        Args:
-            config_files (iterable[str]): A list of the config files to read
-
-            config_dir_path (str): The path where the config files are kept. Used to
-                create filenames for things like the log config and the signing key.
-
-            data_dir_path (str): The path where the data files are kept. Used to create
-                filenames for things like the database and media store.
-
-        Returns: dict
-        """
-        # first we read the config files into a dict
-        specified_config = {}
-        for config_file in config_files:
-            yaml_config = self.read_config_file(config_file)
-            specified_config.update(yaml_config)
-
-        # not all of the options have sensible defaults in code, so we now need to
-        # generate a default config file suitable for the specified server name...
-        if "server_name" not in specified_config:
-            raise ConfigError(MISSING_SERVER_NAME)
-        server_name = specified_config["server_name"]
-        config_string = self.generate_config(
-            config_dir_path=config_dir_path,
-            data_dir_path=data_dir_path,
-            server_name=server_name,
-            generate_secrets=False,
-        )
-
-        # ... and read it into a base config dict ...
-        config = yaml.safe_load(config_string)
-
-        # ... and finally, overlay it with the actual configuration.
-        config.pop("log_config")
-        config.update(specified_config)
-
-        if "report_stats" not in config:
-            raise ConfigError(
-                MISSING_REPORT_STATS_CONFIG_INSTRUCTIONS
-                + "\n"
-                + MISSING_REPORT_STATS_SPIEL
-            )
-        return config
-
     def parse_config_dict(self, config_dict, config_dir_path, data_dir_path):
         """Read the information from the config dict into this Config object.
 
@@ -470,6 +410,30 @@ class Config(object):
         self.invoke_all("generate_files", config_dict, config_dir_path)
 
 
+def read_config_files(config_files):
+    """Read the config files into a dict
+
+    Args:
+        config_files (iterable[str]): A list of the config files to read
+
+    Returns: dict
+    """
+    specified_config = {}
+    for config_file in config_files:
+        with open(config_file) as file_stream:
+            yaml_config = yaml.safe_load(file_stream)
+        specified_config.update(yaml_config)
+
+    if "server_name" not in specified_config:
+        raise ConfigError(MISSING_SERVER_NAME)
+
+    if "report_stats" not in specified_config:
+        raise ConfigError(
+            MISSING_REPORT_STATS_CONFIG_INSTRUCTIONS + "\n" + MISSING_REPORT_STATS_SPIEL
+        )
+    return specified_config
+
+
 def find_config_files(search_paths):
     """Finds config files using a list of search paths. If a path is a file
     then that file path is added to the list. If a search path is a directory
diff --git a/synapse/config/api.py b/synapse/config/api.py
index d9eff9ae1f..dddea79a8a 100644
--- a/synapse/config/api.py
+++ b/synapse/config/api.py
@@ -30,7 +30,7 @@ class ApiConfig(Config):
             ],
         )
 
-    def default_config(cls, **kwargs):
+    def generate_config_section(cls, **kwargs):
         return """\
         ## API Configuration ##
 
diff --git a/synapse/config/appservice.py b/synapse/config/appservice.py
index b74cebfca9..8387ff6805 100644
--- a/synapse/config/appservice.py
+++ b/synapse/config/appservice.py
@@ -34,7 +34,7 @@ class AppServiceConfig(Config):
         self.notify_appservices = config.get("notify_appservices", True)
         self.track_appservice_user_ips = config.get("track_appservice_user_ips", False)
 
-    def default_config(cls, **kwargs):
+    def generate_config_section(cls, **kwargs):
         return """\
         # A list of application service config files to use
         #
diff --git a/synapse/config/captcha.py b/synapse/config/captcha.py
index a08b08570b..8dac8152cf 100644
--- a/synapse/config/captcha.py
+++ b/synapse/config/captcha.py
@@ -28,7 +28,7 @@ class CaptchaConfig(Config):
             "https://www.recaptcha.net/recaptcha/api/siteverify",
         )
 
-    def default_config(self, **kwargs):
+    def generate_config_section(self, **kwargs):
         return """\
         ## Captcha ##
         # See docs/CAPTCHA_SETUP for full details of configuring this.
diff --git a/synapse/config/cas.py b/synapse/config/cas.py
index a5f0449955..ebe34d933b 100644
--- a/synapse/config/cas.py
+++ b/synapse/config/cas.py
@@ -35,7 +35,7 @@ class CasConfig(Config):
             self.cas_service_url = None
             self.cas_required_attributes = {}
 
-    def default_config(self, config_dir_path, server_name, **kwargs):
+    def generate_config_section(self, config_dir_path, server_name, **kwargs):
         return """
         # Enable CAS for registration and login.
         #
diff --git a/synapse/config/consent_config.py b/synapse/config/consent_config.py
index 6fd4931681..94916f3a49 100644
--- a/synapse/config/consent_config.py
+++ b/synapse/config/consent_config.py
@@ -111,5 +111,5 @@ class ConsentConfig(Config):
             "policy_name", "Privacy Policy"
         )
 
-    def default_config(self, **kwargs):
+    def generate_config_section(self, **kwargs):
         return DEFAULT_CONFIG
diff --git a/synapse/config/database.py b/synapse/config/database.py
index c8963e276a..bcb2089dd7 100644
--- a/synapse/config/database.py
+++ b/synapse/config/database.py
@@ -38,7 +38,7 @@ class DatabaseConfig(Config):
 
         self.set_databasepath(config.get("database_path"))
 
-    def default_config(self, data_dir_path, **kwargs):
+    def generate_config_section(self, data_dir_path, **kwargs):
         database_path = os.path.join(data_dir_path, "homeserver.db")
         return (
             """\
diff --git a/synapse/config/emailconfig.py b/synapse/config/emailconfig.py
index 07df7b7173..cf39936da7 100644
--- a/synapse/config/emailconfig.py
+++ b/synapse/config/emailconfig.py
@@ -214,7 +214,7 @@ class EmailConfig(Config):
                 if not os.path.isfile(p):
                     raise ConfigError("Unable to find email template file %s" % (p,))
 
-    def default_config(self, config_dir_path, server_name, **kwargs):
+    def generate_config_section(self, config_dir_path, server_name, **kwargs):
         return """
         # Enable sending emails for password resets, notification events or
         # account expiry notices
diff --git a/synapse/config/groups.py b/synapse/config/groups.py
index d11f4d3b96..2a522b5f44 100644
--- a/synapse/config/groups.py
+++ b/synapse/config/groups.py
@@ -21,7 +21,7 @@ class GroupsConfig(Config):
         self.enable_group_creation = config.get("enable_group_creation", False)
         self.group_creation_prefix = config.get("group_creation_prefix", "")
 
-    def default_config(self, **kwargs):
+    def generate_config_section(self, **kwargs):
         return """\
         # Uncomment to allow non-server-admin users to create groups on this server
         #
diff --git a/synapse/config/jwt_config.py b/synapse/config/jwt_config.py
index a2c97dea95..36d87cef03 100644
--- a/synapse/config/jwt_config.py
+++ b/synapse/config/jwt_config.py
@@ -41,7 +41,7 @@ class JWTConfig(Config):
             self.jwt_secret = None
             self.jwt_algorithm = None
 
-    def default_config(self, **kwargs):
+    def generate_config_section(self, **kwargs):
         return """\
         # The JWT needs to contain a globally unique "sub" (subject) claim.
         #
diff --git a/synapse/config/key.py b/synapse/config/key.py
index 5ec465b196..8fc74f9cdf 100644
--- a/synapse/config/key.py
+++ b/synapse/config/key.py
@@ -122,7 +122,7 @@ class KeyConfig(Config):
         # falsification of values
         self.form_secret = config.get("form_secret", None)
 
-    def default_config(
+    def generate_config_section(
         self, config_dir_path, server_name, generate_secrets=False, **kwargs
     ):
         base_key_name = os.path.join(config_dir_path, server_name)
diff --git a/synapse/config/logger.py b/synapse/config/logger.py
index 3e05f49aba..931aec41c0 100644
--- a/synapse/config/logger.py
+++ b/synapse/config/logger.py
@@ -80,7 +80,7 @@ class LoggingConfig(Config):
         self.log_config = self.abspath(config.get("log_config"))
         self.log_file = self.abspath(config.get("log_file"))
 
-    def default_config(self, config_dir_path, server_name, **kwargs):
+    def generate_config_section(self, config_dir_path, server_name, **kwargs):
         log_config = os.path.join(config_dir_path, server_name + ".log.config")
         return (
             """\
diff --git a/synapse/config/metrics.py b/synapse/config/metrics.py
index 6af82e1329..3698441963 100644
--- a/synapse/config/metrics.py
+++ b/synapse/config/metrics.py
@@ -40,7 +40,7 @@ class MetricsConfig(Config):
                     "sentry.dsn field is required when sentry integration is enabled"
                 )
 
-    def default_config(self, report_stats=None, **kwargs):
+    def generate_config_section(self, report_stats=None, **kwargs):
         res = """\
         ## Metrics ###
 
diff --git a/synapse/config/password.py b/synapse/config/password.py
index 300b67f236..598f84fc0c 100644
--- a/synapse/config/password.py
+++ b/synapse/config/password.py
@@ -28,7 +28,7 @@ class PasswordConfig(Config):
         self.password_enabled = password_config.get("enabled", True)
         self.password_pepper = password_config.get("pepper", "")
 
-    def default_config(self, config_dir_path, server_name, **kwargs):
+    def generate_config_section(self, config_dir_path, server_name, **kwargs):
         return """\
         password_config:
            # Uncomment to disable password login
diff --git a/synapse/config/password_auth_providers.py b/synapse/config/password_auth_providers.py
index 8ffefd2639..788c39c9fb 100644
--- a/synapse/config/password_auth_providers.py
+++ b/synapse/config/password_auth_providers.py
@@ -46,7 +46,7 @@ class PasswordAuthProviderConfig(Config):
 
             self.password_providers.append((provider_class, provider_config))
 
-    def default_config(self, **kwargs):
+    def generate_config_section(self, **kwargs):
         return """\
         #password_providers:
         #    - module: "ldap_auth_provider.LdapAuthProvider"
diff --git a/synapse/config/push.py b/synapse/config/push.py
index 99d15e4461..1b932722a5 100644
--- a/synapse/config/push.py
+++ b/synapse/config/push.py
@@ -42,7 +42,7 @@ class PushConfig(Config):
             )
             self.push_include_content = not redact_content
 
-    def default_config(self, config_dir_path, server_name, **kwargs):
+    def generate_config_section(self, config_dir_path, server_name, **kwargs):
         return """
         # Clients requesting push notifications can either have the body of
         # the message sent in the notification poke along with other details
diff --git a/synapse/config/ratelimiting.py b/synapse/config/ratelimiting.py
index b03047f2b5..8c587f3fd2 100644
--- a/synapse/config/ratelimiting.py
+++ b/synapse/config/ratelimiting.py
@@ -80,7 +80,7 @@ class RatelimitConfig(Config):
             "federation_rr_transactions_per_room_per_second", 50
         )
 
-    def default_config(self, **kwargs):
+    def generate_config_section(self, **kwargs):
         return """\
         ## Ratelimiting ##
 
diff --git a/synapse/config/registration.py b/synapse/config/registration.py
index 6d8a2df29b..4a59e6ec90 100644
--- a/synapse/config/registration.py
+++ b/synapse/config/registration.py
@@ -85,7 +85,7 @@ class RegistrationConfig(Config):
             "disable_msisdn_registration", False
         )
 
-    def default_config(self, generate_secrets=False, **kwargs):
+    def generate_config_section(self, generate_secrets=False, **kwargs):
         if generate_secrets:
             registration_shared_secret = 'registration_shared_secret: "%s"' % (
                 random_string_with_symbols(50),
diff --git a/synapse/config/repository.py b/synapse/config/repository.py
index 43e6c4921f..80a628d9b0 100644
--- a/synapse/config/repository.py
+++ b/synapse/config/repository.py
@@ -190,7 +190,7 @@ class ContentRepositoryConfig(Config):
 
             self.url_preview_url_blacklist = config.get("url_preview_url_blacklist", ())
 
-    def default_config(self, data_dir_path, **kwargs):
+    def generate_config_section(self, data_dir_path, **kwargs):
         media_store = os.path.join(data_dir_path, "media_store")
         uploads_path = os.path.join(data_dir_path, "uploads")
 
diff --git a/synapse/config/room_directory.py b/synapse/config/room_directory.py
index 24223db7a1..a92693017b 100644
--- a/synapse/config/room_directory.py
+++ b/synapse/config/room_directory.py
@@ -46,7 +46,7 @@ class RoomDirectoryConfig(Config):
                 _RoomDirectoryRule("room_list_publication_rules", {"action": "allow"})
             ]
 
-    def default_config(self, config_dir_path, server_name, **kwargs):
+    def generate_config_section(self, config_dir_path, server_name, **kwargs):
         return """
         # Uncomment to disable searching the public room list. When disabled
         # blocks searching local and remote room lists for local and remote
diff --git a/synapse/config/saml2_config.py b/synapse/config/saml2_config.py
index d86cf0e6ee..872a1ba934 100644
--- a/synapse/config/saml2_config.py
+++ b/synapse/config/saml2_config.py
@@ -61,7 +61,7 @@ class SAML2Config(Config):
             },
         }
 
-    def default_config(self, config_dir_path, server_name, **kwargs):
+    def generate_config_section(self, config_dir_path, server_name, **kwargs):
         return """\
         # Enable SAML2 for registration and login. Uses pysaml2.
         #
diff --git a/synapse/config/server.py b/synapse/config/server.py
index 1e58b2e91b..2f5d1a6ae3 100644
--- a/synapse/config/server.py
+++ b/synapse/config/server.py
@@ -307,7 +307,7 @@ class ServerConfig(Config):
     def has_tls_listener(self):
         return any(l["tls"] for l in self.listeners)
 
-    def default_config(self, server_name, data_dir_path, **kwargs):
+    def generate_config_section(self, server_name, data_dir_path, **kwargs):
         _, bind_port = parse_and_validate_server_name(server_name)
         if bind_port is not None:
             unsecure_port = bind_port - 400
diff --git a/synapse/config/server_notices_config.py b/synapse/config/server_notices_config.py
index 05110c17a6..eaac3d73bc 100644
--- a/synapse/config/server_notices_config.py
+++ b/synapse/config/server_notices_config.py
@@ -78,5 +78,5 @@ class ServerNoticesConfig(Config):
         # todo: i18n
         self.server_notices_room_name = c.get("room_name", "Server Notices")
 
-    def default_config(self, **kwargs):
+    def generate_config_section(self, **kwargs):
         return DEFAULT_CONFIG
diff --git a/synapse/config/spam_checker.py b/synapse/config/spam_checker.py
index 1968003cb3..e40797ab50 100644
--- a/synapse/config/spam_checker.py
+++ b/synapse/config/spam_checker.py
@@ -26,7 +26,7 @@ class SpamCheckerConfig(Config):
         if provider is not None:
             self.spam_checker = load_module(provider)
 
-    def default_config(self, **kwargs):
+    def generate_config_section(self, **kwargs):
         return """\
         #spam_checker:
         #  module: "my_custom_project.SuperSpamChecker"
diff --git a/synapse/config/stats.py b/synapse/config/stats.py
index 73a87c73f2..b518a3ed9c 100644
--- a/synapse/config/stats.py
+++ b/synapse/config/stats.py
@@ -42,7 +42,7 @@ class StatsConfig(Config):
                 / 1000
             )
 
-    def default_config(self, config_dir_path, server_name, **kwargs):
+    def generate_config_section(self, config_dir_path, server_name, **kwargs):
         return """
         # Local statistics collection. Used in populating the room directory.
         #
diff --git a/synapse/config/third_party_event_rules.py b/synapse/config/third_party_event_rules.py
index 1bedd607b6..b3431441b9 100644
--- a/synapse/config/third_party_event_rules.py
+++ b/synapse/config/third_party_event_rules.py
@@ -26,7 +26,7 @@ class ThirdPartyRulesConfig(Config):
         if provider is not None:
             self.third_party_event_rules = load_module(provider)
 
-    def default_config(self, **kwargs):
+    def generate_config_section(self, **kwargs):
         return """\
         # Server admins can define a Python module that implements extra rules for
         # allowing or denying incoming events. In order to work, this module needs to
diff --git a/synapse/config/tls.py b/synapse/config/tls.py
index 9a66e8cc4b..8fcf801418 100644
--- a/synapse/config/tls.py
+++ b/synapse/config/tls.py
@@ -217,7 +217,9 @@ class TlsConfig(Config):
             if sha256_fingerprint not in sha256_fingerprints:
                 self.tls_fingerprints.append({"sha256": sha256_fingerprint})
 
-    def default_config(self, config_dir_path, server_name, data_dir_path, **kwargs):
+    def generate_config_section(
+        self, config_dir_path, server_name, data_dir_path, **kwargs
+    ):
         base_key_name = os.path.join(config_dir_path, server_name)
 
         tls_certificate_path = base_key_name + ".tls.crt"
diff --git a/synapse/config/user_directory.py b/synapse/config/user_directory.py
index 0665dc3fcf..f6313e17d4 100644
--- a/synapse/config/user_directory.py
+++ b/synapse/config/user_directory.py
@@ -33,7 +33,7 @@ class UserDirectoryConfig(Config):
                 "search_all_users", False
             )
 
-    def default_config(self, config_dir_path, server_name, **kwargs):
+    def generate_config_section(self, config_dir_path, server_name, **kwargs):
         return """
         # User Directory configuration
         #
diff --git a/synapse/config/voip.py b/synapse/config/voip.py
index 01e0cb2e28..2ca0e1cf70 100644
--- a/synapse/config/voip.py
+++ b/synapse/config/voip.py
@@ -26,7 +26,7 @@ class VoipConfig(Config):
         )
         self.turn_allow_guests = config.get("turn_allow_guests", True)
 
-    def default_config(self, **kwargs):
+    def generate_config_section(self, **kwargs):
         return """\
         ## TURN ##