Sounds like shortening the stoker compartment from 32" to 30" has been good for you and a good tradeoff it seems.
Staying with the 32" would have meant using 2" dia top tube instead of 1.75" to get the stiffness you needed - any downside to using the 2" instead of the 1.75" to get the 32" you had originally spec'd?
We have a shorter stoker compartment - only 27" - and my 5'-2" stoker rides in her most comfortable position and we never have the stoker hands / handlebar / captain's legs issue but maybe we get away with it because of the handlebar she uses. Instead of drop bars with dummies or bullhorns she has a variation on a flat bar designed by Jitensha Studio, made by Nitto, I believe. The bar is positioned at about the same height as her saddle. Her frame of reference is her commuter bike (she doesn't have a conventional road bike with drops) which has a flat handlebar but her stoker bar gives her more options on hand positioning, but not like drops of bullhorns would, nonetheless it seems to work well for her. No complaints on centuries anyway - we'll see when we move up to double centuries this summer.
It is fascinating the way different setups are preferred by different teams and the process by which they arrive at their chosen configurations. Also interesting to note that you designed the bike the way you would use it the vast majority of the time which I think makes great sense. Sometimes it seems that teams design to cover every contingency, which may seem prudent, but perhaps the main objective may be compromised a bit.
The thread has wandered far from the original question (as oftern happens) but is still interesting!