Why can’t the save game and config.ini just be in the main god damn game directory?

You'd lose all save games every time you uninstall the game. We already had that in DOS/Win9x days and I am very happy that we moved away from this. Static program data and generated data should be clearly separated.

In Linux we have the XDG Base Directory spec for that, that gives you directories for cache, config, state and data, so everything is nicely separated. The only problem is that not every app follows it, bug reports can help.

I find Android handles this by far the worst. They have the core right idea with permissions that makes it impossible for games to write outside of their assigned directories, but the way they handle it your savegames go into an area that will be deleted when you uninstall the app. So the risk of losing savegames is extremely high. The alternative is that games require SD card permissions and than just write wherever they want. It's basically all just a dark pattern to force games into using the Google Play service for cloud saves. Games that lose state and restart when you switch apps are also great.