@Val9613, the custom firmware is nothing 'magical' or 'special', it's basically a hack in the Atgames menu to allow other file extensions to be loaded. Some other changes are the support to load the rom partition from the SD Card or use PicoDrive instead of Genesis Plus GX.
The 'retroplayer', which is responsible to load the libretro core, detect and configure controllers, etc., is not not touched at all.
I can't tell you if other controllers will work, I assume they will not or the lack of buttons would cause issues. You can try by yourself if you have them.
The ROMs will likely work, Master System works with restrictions (PAL games have audio delay or don't play well), and I've never tried to run SG-1000 games.