Thanks for the pointers, that was one of the things I was hoping for. (Yes indeed I have already been about this topic, since it’s a thing that often pops up when fixing packages that have oiptional features. Actually the trigger was my renewed interest in deploying a headless calbre server, you might even vaguely remember the related PR (as yet unresolved) 
).
I hope we’ll have at least one potential solution (I didn’t have time yet to study the details of RFC169 and nixpkgs#312432 yet).
Probably it doesn’t even have to be an all or nothing solution from the start, any de-duplication of same-use-different-name flags could constitute a win, even if nothing else would change. So specific PRs for improvement could coexist with (the IMO very much needed) development of a more fundamental solution.