@twh_pi actually there is already a way to override libretro configurations on a per folder basis. Unfortunately, it doesn't work for Atari 8bits because it relies on its own configuration file.
We should add code in the emulator launcher to keep libretro and proprietary configuration synchronised so that people could make sub-folders with specific machine-configs.
This is already working for the c64. You can make machine-specific sub-folders to get the emulator automatically emulate Pet, Vic-20, CBM, c64, c128 etc...
This is an undocumented feature yet, and we have to rewrite several parts of the WIKI!
PS: I had several friends having an Atari 800XL in my yougness, and some of them bought a 130XE later. AFAIR, there is some compatibility issues. That's why we choose the 800XL since this is the most common machine, at least in Europe.