@meleu
You rock. Thanks for the clarity.
Now say someone wants to use RetroArch's functionality for override config files... Haha, only joking. I don't really want to go down that road, but if anyone is curious there is yet another way to manage configs in RetroArch called override files. I won't even pretend to understand the behavior when trying to use those in RetroPie, but I know some people use them on other platforms.
For override files, I believe you just put whatever changes to settings you want in there, and it will override those specific settings in the global config settings on a per emulator basis. This sound remarkably a lot like the way RetroPie manages configs!
I need a drink.