hmm, i think if retroarch can’t tell the difference between the pads then you may struggle.

can’t you just set up each /opt/retropie/configs/SYSTEMNAME/retroarch.cfg with the correct input settings for the controller you want to use for each systems? you could do this through the retroarch UI within the emulators if you preferred. then it’d be right as long as you had the right one plugged in for each system.