there is, but there’s currently a bug with it: https://github.com/RetroPie/RetroPie-Setup/issues/899

that said, i have the same controller and mario all stars works fine for me in snes9x (which I think is the default?). perhaps you’ve accidentally created a rom-specific config for this, which it’s using instead of the proper one, causing neither to be read, or some other weird issue? if you look in your roms directory, is there a .cfg file with the same name as the rom?