It works by having only the right pad for the console plugged in at a time. I'll stick to that since my daughter has a USB hub with a switch for each port on her Pi. So I can have all pads plugged in at once but only use the one I want thanks to the power button on the hub.
I've set up four kinds of pads: a NES pad, 3 SNES pads, a N64 pad and a Megadrive pad. Thanks to your setup (with retroarch.cfg files) I don't have to map the pad buttons anymore: I can just power them on and off with the button on my hub and enjoy any console that I like.
Thank you so much for my daughter & cheers from France! :-)