necrobumping my own post because I found a workaround.
I use runcommand-onstart.sh script (docs : https://github.com/RetroPie/RetroPie-Setup/wiki/Runcommand , my script : https://pastebin.com/XunR2bBY) combined with some delay (hard programmed in my fanControl program) to relaunch fanControl after Mupen has done its shenanigans and thus reclaim the GPIO.