But that's the problem. You've just turned every military ship into more of a multipurpose. It imbalances what balance there is supposed to be.
Well, first, I believe that balance in this game is a broken concept in any case. There is always a meta dynamic, no matter how you set up ship use.
"Rebalancing" against this would simply involve moving the Mil IC up or down the scale to make it appropriate.
Personally, I still would rather have volume based design on a base frame, but, since that seems unlikely, I think that, if you are going to artificially restrict spaces to certain equipment, if SCBs are military, shields themselves should be as well.