Seriously, since late Windows 95 era we have this thing called USB ports. That means you can attach and detach controllers at will without rebooting the PC (for the emulator it could be a different matter, but everything is controlled by a front-end so that doesn't matter).
It wouldn't hurt to make detachable control panels with USB ports for every possible configuration you would like and have them shelved next to the cabinet for the very rare cases you would need a special out of the ordinary set up changed in less than 10 seconds. Making the cabinet comfortable too.
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