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My recommendation would be to stop trying to fight RetroPie for control of the configs. Why do you want to change the location of the configs? Why do you want to enable save on exit? If you don’t want RetroPie to be RetroPie, install Raspbian and then install RetroArch on top of that and be done. It will act just like your Windows installation of RA.
If you take my advice, then the layout of the configs is pretty straight forward. /opt/retropie/configs/all/retroarch.cfg is the main config file
The individual system configs, for example /opt/retropie/configs/nes/retroarch.cfg override the main config file (just like it says in each of these files)
# All settings made here will override the global settings for the current emulator core
if you run jstest and determine your button mappings you can modify the main config /opt/retropie/configs/all/retroarch.cfg. For example, if you have two buttons to spare and don’t want to use a hotkey:
input_enable_hotkey_btn = nul
input_menu_toggle_btn = "14"
input_exit_emulator_btn = "15"
RetroPie is designed to not use the RetroArch GUI – RetroPie is designed to be a 10 foot interface and the RA GUI is not a 10′ friendly interface. If you want to make changes, settings should be made in the config files, settings made via the GUI will not be saved. If you try to change that behavior, you’ll have to hack up ES – the commands it uses to launch RA are hard coded with the locations of the cfg files it is designed to use.