Is this something that still might get done? If it made it easier, perhaps a first step could be just to check for a bunch of constants before including each add-on? Then developers could set those constants to effectively remove add-ons from the available list?
I’d be happy to help, if there was a chance of getting something like this into the premium plugin soon.
In the meantime, I guess I’ll just remove admin menus and customizer sections for safety. That’s just a bit potentially confusing for any client who tries to enable an add-on and can’t understand why its settings are not showing up – so not ideal.