The way this is shaping up is towards a generalised, decentralised Engineering Hull - which I like a lot!
At first I was unsure about scattering the crystals around different rooms in the ship. To my mind, all 4 crystals would be together, in that pop-out box from Elaan
(we just only ever saw the top quarter of the holder).
However, this is starting to make sense to me - different engineering sections which ordinarily control their own parts of the ship (Impulse Engines, Deflector, port & starboard Nacelles) but which can (if neccessary) take over the workload for other areas during maintainence (or crystal failure). Scotty could be in any one of these Engine Rooms at any given time, depending on what was needed.
The phrase "I'll be in Engineering" now means he'll be in a rough area of the secondary hull (or saucer) rather than a specific room and when Scotty talks about his "Engine Room" (singular) he is simply referring to whichever one is required for that particular task - everyone would know which one he was referring to, hence no further elaboration is needed.
So, what of the bypass / convertor assembly? How does that
fit into this engineering sprall? I think it must be at the central convergence of the energy transfer, otherwise it couldn't actually bypass
anything. Perhaps it too has its own engine room?