"I’m curious if anyone else had noticed the low crown height positioning with Ruby cases?"
Not with 'Ruby' cases (never owned one) but others, some supposed to be from 'JKF' etc. My supposed 'JKF' case has a lower case tube hole btw.
I will always believe the high $$ cases are stock cases from various makers that are skillfully detailed to be high $$ cases and they can come with higher or lower case tube bores. This can be compensated for by the internal machining.
My Yuki 5512 and 5513 cases from May 2014 have higher case tube bores and the fit and finish is some of the best I have seen to date. Yuki no longer sells cases however.
My MBK cases are made for a rolex 1570/75 date movement or ETA 2836, even when the cases are signed 5512 or 5513 and they have slightly lower case tube bores to accept the .4 or .5mm thicker rolex date movement or ETA 2836.
I never paid very much attention to higher or lower crown positions and just go with what I get.
Imho (and from past experience) the luck of the draw determines what you end up with.