I've settled on there being three "engineering bays" aboard Enterprise which were represented by the same set. Ultimately, the idea is that the basic room layout we saw was based around servicing an "energizer" (the rows of tubes)... with the "energizer" being what converts the raw output of the reactors into useable energy which can power various ship's systems.We have to remember that Engineering was always described as an expansive maze where Evil Kirks or Ben Finneys could hide almost indefinitely. None of the sets really caters for that. But none of them features even three full walls, let alone four. We'd be fully within our rights to assume, then, that the sets only represent a tiny fraction of the entire space - and not necessarily the same fraction every time, either!
There could well be half a dozen rooms like the one we usually see, some with the two merged pillboxes in the middle of the floor, some without; some with alcoves and consoles arranged as the Chief Engineer's personal workplace, some without. And those would be just the control rooms that are specifically made aesthetically and ergonomically pleasing; the rest of Engineering could be a maze of spars and pipes, much like the one we saw in the newest movie.
A combination of "they are different rooms" and "they are being modified during the mission" would probably be worked out, so that there'd be a set number of Engineering locations visited, with a set number of modifications made to some of them.
Timo Saloniemi
In my case, I have one in the secondary hull, with the energizer nestled between the warp nacelle pylons, and with two additional bays in the primary hull, to either side of the impulse engine deck, tangent to the primary hull OD.
The functions of the three rooms are somewhat parallel (remember, most control systems on the ship are computer-based, and consoles are simply computer terminals). The only major difference is what physical hardware is adjacent to each one.