I know next to nothing about this, but it occurs to me you might be able to change the moves / weapons / whatnot of the shipyards in their defs file so that they could function like a more regular starship? Might never be able to adjust/evolve them though, but if you're content with having a uniform hive-ship it might work.
Or to say it another way: It might work better to make a shipyard with starship functionality than make a starship with shipyard functionality.