Slight misunderstanding here
Any ship design, that incorporates an orbital habitat can be build by your construction factories on planet.
If you pre-build ships parts with your industry, those parts are automaticaly used by your shipyards, when you order a ship build, that uses those parts.
Prebuilding, for example, engines, can speed up construction of your warfleet by quite a bit.
Edit: Rereading what I wrote, it is not as clear as I thought.
Yes, you design a ship(base) which holds the habitat. The finished design will then be build by your construction factories.