Just an update. I'm spending what free time I have mostly catching up on episodes that had the engineering section in it. That way I can see how wide the engine room would be in the engineering hull as well as whether the "big vertical pipe" would be visible in S2/S3 from the manual monitoring room on the other side.
So far my current thoughts are for two engine rooms with identical starboard sides as seen in the show. The primary hull one doesn't have the big vertical pipe while the one in the engineering hull does. The vertical pipe connects machinery below the deck to the engineering room in the deck above with the Energizer as seen in "The Alternative Factor". From there, the primary energy circuit then runs up through the neck to the primary hull engine room.
For S2 engine room in the engineering hull, the Energizer is moved down and incorporated into the structure in the center of the room and the energizer room above is removed to make room for the taller engine room ceiling.
Well, that's where I'm heading anyway. Everyone have a great Memorial weekend!