I’m actually rebuilding the whole board again so I haven’t tried different caps yet, but I can confirm a method that worked for me to resolve the issue:
Aside from burnishing the small amount of flash on the bottom edges of the caps (flattening the thin ridge of plastic that sticks out), I made sure to gently pull the bezel outwards when tightening the two middle screws.
I did this on both long-edge bezels, being sure to only tighten the screws enough so they won’t back-out - they don’t need to be very tight at all thanks to the many threads and gaskets adding tension.
I did take a comparison photo of an MT3 cap vs a Cherry profile IFK one, and they are a hair taller from front to back:
All edges are flush aside from what’s sticking out there - between that fraction of a mm and the natural warping of polycarb, these caps rub on that case until you take a step or two to prevent it.
Edit: as for the stab rotation issue, I have some info on that in the MT3 ‘rubbing’ thread.