From what we've seen in the Rogue Trader rulebooks, the parts within a ship are pretty variable. Someships come with parts that can not be removed (like the Dominator class cruiser and its additional flight decks), but a lot of other parts can be swapped out (life support, engines, weapon arrays, additional armor, ect.)
Certain vessels ARE STC. We know that Astartes strike cruisers and battle barges tend to be STCs.
Many others are not. Just like many things in WH40K, it mostly depends on the precise situation.
Certain vessels ARE STC. We know that Astartes strike cruisers and battle barges tend to be STCs.
Many others are not. Just like many things in WH40K, it mostly depends on the precise situation.