Bill, you’re such a fine, meticulous baker, that it’s hard to imagine you having any problems! 
I don’t know if any of this will help, but I’ll throw it out there just in case:
-Maybe slight overbaking? Have you noticed that the ones in the middle of the pan shrink less? That might be a sign of overbaking. I know you’re very meticulous, do you take an internal temp when they’re done? For cupcakes especially, I like them to just reach 190F.
-Maybe it has to do with goals: I like my cupcakes gently rounded and just full enough to rise up over the lip of the paper. Are yours flat and less full?
-Does the creaming method seem to help? I would imagine that it works in the other direction- more gluten could mean more shrinking, but I know you prefer it so it must help.
I like the buttermilk country cake and the chocolate fudge cake as cupcakes, have you tried those? They both have acidic ingredients (buttermilk, brown sugar), I don’t know, but maybe that helps the eggs set well enough, combined with the slight underbaking, to limit shrinking.
I think, at least in my kitchen, that the domingo base is more likely to crack and pull away from the wrappers. It’s a richer cake, so maybe it comes down to fat content? Kind of like pie crusts that don’t stick to pans if they’re rich enough?
