If I were to take a guess at this, I would suggest that when the ssh client is using a configuration from the default locations, the user initiating the connection isn't really aware that a configuration file is being used. There is an implicit assumption that the config file hasn't been tampered with. If the permissions are too permissive, then that may mean the user is trusting the default config is safe, when it isn't.
When you reference a config file with the
-F option, you are explicitly saying that you want that configuration file. You are basically telling the client, that you know what you want, and that configuration file is it. You have the responsibly to know what you are doing. There are valid use cases where a group of people might want to share a common configuration file for a set of common servers.