I had the craziest of ideas but since Trek has both transporters and replicators could you have on file a range of shuttles and ships and then replicate specific shuttles for specific missions, or small ships as needed on demand? You could use maybe stored data patterns so you could "beam them out" into the shuttlebay or outside the ship, or replicators to fabricate them as you build them section by section.
Could this be done?
Could this be done?