Your study was a superb example of geekhackery, Photoelectric. We really needed these closeups.
I, too, had been wondering why my clears seemed to have more problems with keycaps.
This is not something most people can just tell at a glance. (EG you had to zoom in with camera to show the bigger clears bump.)
But when that's said and done, I have had vintage clears and new clears, and on different keycaps, they were never so tight as to have serious problems. At worst it was only 'harder to pull out'.
I'm wondering if there is a problem with Terran's custom made keyboard. Too bad they are doubleshots. If they were PBT I would suggest heating them slightly to see if they can expand and be removed more easily.
Terran, I'm thinking of one possibility. Try it on a spare switch first. Put a stem in the fridge to cool it, then use a bit of lube, and see if you can push it back in from the top. Otherwise you have to desolder both switch and LEDs.
I've had it with many different keycaps. The only ones that have been okay so far have been thick Vortex PBT dye sub caps.