So Miniaturization and capacity seem to be unified under the way the system currently works.

If I build the Hyperion Shrinker and surround it with Military stuff, I can get my medium size ships that start out with 50 capacity to suddenly have 180 or more capacity.

This is counterintuitiive on several levels mostly with the fact that we can stick things like Carrier Bays, and Transport pods and things that realistically can not be 360% smaller and still hold people. 

Also weapons such as mass drivers and missiles need mass to be effective.   

I think it would be better if the research gave two different approaches.  

1.  Miniaturization which actually reduces the size of the components we put on the ships.    Life support A was 10.. now it is 6 
2. Capacity/Efficiency bonuses, which increase the available space on a ship.

If the computers on a ship once took up a whole room... but now take up a slot the size of a cell phone.... then hey we can fill that room with warheads now right?

Just some thoughts.