I agree; not the end of the world, but it is nice to be able to control the master level of the relative magnetic and piezo balance. Some folks don’t like a pot where the master level pot is located, so they unscrew the washer, push the pot into their Fly, and plug the hole.
I’ve plugged the switch and “red button” stereo switch holes with these kinds of plugs. All pots have a 3/8” hole; all switches have a 7/16” hole, the red piezo switch cavity is a 1/2” hole.
I’ve also installed a killswitch in one of mine in the tone pot position; why not?!
Those are the major differences; the refined controls also have a coil-tap option for the magnetic pickups, though I can’t recall if that’s available for all refined Fly models or just the Fly Mojo.
The Powerchip usually comes with the smart jack, and you would not need the red stereo button. You can remove it and plug up the hole, or, as others have shown: makes a great location for a MIDI output port.