The interior of the castle really seems to just be designed with the “boss arena” aspect in mind more than anything else, similar to the Scorpion-7 boss arena, and both versions of the Aegis excavation site boss arena (although those weren’t necessarily designed by Nelson).
So it may just come down to “gameplay” first, and it was more practical for it to not be part of the environment. Lot easier on Nelson to do boss fights in a completely separate environment, and a lot less cheesing can happen like that too.