In TMP, we saw engineers working in spaces that were not "main engineering", but rather the "inner sanctum", because the ship was still in the process of being built and tested. The real Main Engineering of that ship was a room not unlike the TOS one, with tidy control consoles far away from the glowy bits, requiring no radsuits or other protective measures. It just wasn't featured in the movie.
In ST2:TWoK, we again saw the interiors because this was a training cruise where emergencies and nonstandard procedures as well as the deepest inner workings of the ship were the target of training. In normal ops, Scotty would rarely don a radsuit and enter these spaces.
Possibly the real Main Engineering was seen in ST6:TUC, featuring just a single thickly protected section of the vertical power conduit, or perhaps the actual reactor part. (That is, the barely glimpsed TNG set reuse was the shirtleeves part of the TMP setup.)
At the moment I'm drawing a blank on engineering in ST6, and considering that's the 1701A not the refit 1701 (and might have a completely different arrangement) for the moment I would prefer to leave it off the table.
What you say is possible. If true, either the "true" Main Engineering (ME) is not connected to the intermix shafts (which would mean it has nothing to do with warp power, other than control), or the vertical intermix shaft goes down and connects to it at the front of the secondary hull (we do not see a rear vertical intermix shaft going down, AFAIK). The second problem is that the spaces where Secondary Hull ME allegedly was now encompass the ST:TMP rec deck (which is at least two decks high, and watching the other night I was leaning towards 3 or more), and perhaps surrounding compartments (seems wider, but who knows -- we never really see all of TOS ME). What we do see in ST1+2 is the long shaft on the dorsal spine and the shaft going upwards, but I'm not sure (without references) that we see a shaft going downward
As a counter-counter point, it occurred to me on the way home that the actual M/AM reactors could
still be in the nacelles, warp plasma is being fed by the shafts as a power source, and its the "main energizers" (power converters?? downgrading warp plasma to standard EPS plasma concentration?) and perhaps not the main reactor that's being fooled around with in the movie. But I'm not claiming that's the case. I'm happy to believe something in the secondary hull of the movie 1701 is a M/AM reactor, I'm just not sure what.
From a personal point of view, in TMP the logical place for the actual "reactor" where the M/AM merge is closest to where it is needed, i.e., the nacelles, which inside the ship would be the junction of intermix shafts that lead up to the nacelle pylons (i.e., the background shot in ST:TMP). But that's just theoretical. Perhaps the added protection of the interconnecting dorsal was a consideration, or they couldn't find short enough engineering candidates to go back there.
Additionally, if there is a traditional ME in the middle of the Secondary hull, I would have placed the warp intermix shafts there to keep them as far away from enemy fire as possible, until the point they actually have to be routed out to the nacelles. So the shaft would run the deck above or below ME, or in-between decks (giving fans of horizontal Jefferies Tubes hope). Not
all the way up to the dorsal and then down its back, as this puts it adjacent to the outer hull for a long distance. Unless its meant to be jettisoned, which I doubt.
IMHO, of course -- i.e., my best guess.
What's going on in TAS?
I'm voting on it being a distillery. Its hard to get good Scotch whiskey in deep space you know.
But in seriousness, whatever this is its been added
to (what appears to be) ME some distance from our beloved "tube room", hasn't replaced anything, isn't glowing, and I would need to study it in much more detail before I could say its an intermix shaft let alone a M/AM reactor. I'm not in favor of ignoring TAS, by any means, at least on general principles.