nah, let them be targeted by stealing ships. the pilots would board the ship, the appropriate ships would be destroyed, then the flag ship would explode killing everyone on board!
i like the limiting idea, but maybe limit it to 1 per planet or such so its not like a "have to have one in every fleet" type thing.
i'd probably more like an idea that 'forces' xan to research siege hulls and have to build those factories
this could quite possibly do it, if the other races didn't have to do any additional research to produce the ship.