It would be great if we could flip a physical switch on the outside of the cabinet to activate a software switch – If not that then a menu setting within the retropie settings would do just fine as well!
It wouldn’t be hard to do just that, assuming you can start the arcade joystick drivers from command line. Just use a python script that starts via /etc/rc.local and evaluate the state of a switch connected to the gpio and start one driver or the other based on that evaluation.
Here’s a little info on working with the gpio. Obviously, you’d want a toggle switch here rather than a tactile switch.