I'm only going to address one point, because I haven't thought about this enough to have nuanced responses - I"m guessing that in part Steve Rogers gets taller because it is about mapping to the genetic potential rather than the achieved phenotype, such that due to poverty nutrition and his other identified medical issues, he did grow as much as he might have. Which kind of goes to the 'genetic map' aspect.

(quick thought about wisdom teeth - do they come out in bad places because size of jaw and sum of size of teeth don't match? is there a way that the genetic map could be tweaked so what you end up with is people who have the full set of teeth without mucking much with the jaw?)

And I remember an SGA story where Rodney gets accidentally treated by one of the magic healing machines, and is horribly traumatised to have his breasts back again when he had gone to such effort to get rid of them.