It saves me from having to balance the ships and hulls separately; if the weapons are built-in, it means that the only "legitimate" combination is as a unit, and that's much easier to balance against vanilla. I don't know if you've considered how much time it would take to properly balance every ship and weapon in the game, but the math is somewhat frightening.
After I arrived at this decision, I decided that even if I had time to do it, I'd like to do it this way anyway because of lore. It makes sense to me that their shipbuilding would be smaller-scale and more streamlined than other factions', since their ships would in theory be built while the fleet is in motion.
