Many settings that “can’t be adjusted” in muOS can be changed in Retroarch directly. And if settings need to be changed across all systems, Retroarch can be accessed in the App menu. Once your global settings are in place, any changes you make in an individual console can be set as a custom override, which plays nicer than a custom config.
If you screw up your Retroarch settings and don’t know how to fix it, you can restore the muOS Retroarch defaults in the task toolkit (also available in apps). You don’t need to perform a reflash to fix this.
DON’T DO THIS INSIDE RETROARCH. That will remove all of the tweaks that have been made to ensure that it runs properly on your device. A lot of work has gone into this.
Once you have all of your settings the way you want, you can save that as a configuration profile under Customisation. If you ever break Retroarch by messing with the settings, you can restore it from here.
For example:
I sync my saves with a PC running Batocera that’s connected to my TV at home through Syncthing. Batocera expects saves to be stored in a folder that matches the name of the source ROM folder (GBC is the ROM folder, so the save folder is called GBC as well). By default, muOS has the saves stored in a folder that matches the given emulator. So when I do a fresh install, one of the first things I do is launch Retroarch and change this setting. Once that configuration is saved, it works across all systems.