@Mytran - That makes sense on the transporter rooms. The ship probably only has one transporter circuit that is shared between the multiple transporter rooms so they might do something like the one that is active has priority. The circuit seems to support de-materializing more than 6 people at a time ("Day of the Dove", maybe even other eps) but perhaps the safety limit is to materialize only 6 at a time?
@BK613 - I like the idea of equipment not necessarily mirrored but for now I'm going to mirror the engine room itself for placement just to see how far I can take it
Right now, I'm working on the idea that the Engine Rooms seen in "The Naked Time" and "The Ultimate Computer" are in the primary hull while all the other rooms more than likely are from the Engineering hull.