You can use all the boffs from both ship and shuttle on either. Kind of a fun bug but everyone will be buying delta fliers for their shuttle if this went live.
I confirmed that it is adding all of the stations from the shuttle to both of them. If you pick a small craft without boff slots your slots on your main ship drop back down to normal. You would end up with 7 boffs on an oddy if you had a the delta flyer set as your small ship.