That would indeed be cool. However, I think it would need a change to the underlying emulators. It would be possible if they could accept command-line parameters.
On my Ubuntu Desktop machine, I have fs-uae for amiga emulation which you pass a configuration file containing the details of your floppy drives, memory etc. This works a treat on EmulationStation. Sadly, I don’t think fs-uae is available for the Pi :/