I have found the sequence that produces this bug.
If you create a new ship, the components you place on the ship sizes correctly. If you upgrade the ship, component sizes are still correct.
However, if you load a game and open the ship designer,
upgrade an existing ship, then the ship components are smaller than advertised. It seems it neglects to add the hull size modifier for the components, ie. Anti-Mat Torpedo: 9+2% Hull Size on a Large 55 Space Hull should take up 10 space, but only takes up 9.
I couldn't figure why this was happening before, so I was able to create some ridiculous ships. On a 220 space Huge Hull (yeah, tons of miniturization), I loaded it up with Black Hole Generators (attack 16, base size 6, 2.67att/size!!! easily most space efficient), and made a 0/0/224 attack, 108/100/100 def ship. It required over 6000 manufacturing points to build, and 80k to buy outright (I had the money

). I also had 3 military star bases, so the ship ended up having over 500 attack and 200 def each type. Oh yeah, it was also blazing fast at 36 speed.
Now, I feel kinda guilty since I've figured out what's wrong. Probably not going to build something like that again.