@herb_fargus to avoid this confusion I've just made a PR to explicitly use rgui as the menu_driver.
https://github.com/RetroPie/RetroPie-Setup/pull/1674

Its this sort of thing that would be good to avoid:
https://retropie.org.uk/forum/topic/3654/i-did-retroarch-updates-and-now-i-can-t-exit-games

@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.

@smoothmalik This is a SOLVED topic. You have to start a new thread describing your problem.

I updated the first post of this thread with some useful informations. This can clarify some things.