"Is "Warp Engine Room aft" the same as "in the saucer"? Because that's the only place the "The Ultimate Computer" engine room fit can be due to that long curving hallway they used so prominently in the episode. That would put at least one Season 2 style engine room in the primary hull."
No, not necessarily. I addressed the issue of reducing corridor radius in theory # 4 in the introduction to my parallel thread: http://www.trekbbs.com/showthread.php?t=195496
Add to this we have seen circular corridors in the engineering hull in "Dagger of the Mind", "The Doomsday Machine", "Mudd's Women" and "The Enemy Within"), therefore it has
to be equally possible to have the corridor leading to the engineering room in "The Ultimate Computer" in the engineering hull, too.