I... don't understand your problem. Is it a PITA to split settings files every single time you start a new project? Yes, sure. Does it take more than five minutes to do so? No.

Really, Flask's config options are better, but they aren't that different from Django. Use the default settings, tell Django which settings to use from the commandline or specify an environment variable pointing at the settings to use. Where you put those settings is completely up to you - nobody's saying they absolutely positively must be part of your repo.

When you're working with multiple environments you'll have to specify which configuration to use one way or another so I'd prefer it to use the least amount of abstraction.