I don't think there's anything in any of the films themselves that settles where the M/AM reaction occurs on the refit Enterprise; one could arguably make the same claim for both TOS and TAS, despite strong suggestive evidence otherwise.
I don't think TWOK's radiation room scene makes any sense if the M/AM reaction is in the nacelles instead of right there in main engineering. If that were the case, then Spock would need to work up in the nacelle(s), as that's where both reactor and engine is.
Not that it makes any sense as-is... but it makes less sense that way.
Not necessarily. We don't know why the engines are offline in TWOK, at that point in the film.
Maybe the refit analogs of the dilithium crystals shown in Elaan of Troyius
just need to be put back into place. Maybe that's what Spock is fiddling with in the thing he opens: some crystals in some sort of setting. That would be consistent with everything we see and hear on screen in TWOK. We never get a good look inside the thing he opens, and they never say on screen what it is, either, IIRC.
Don't get me wrong. I'm not arguing for the layout to be different from what we know it to be. But we "know" what it is based on all the various tie-in material and statements of intent from the designers, not from what's shown on screen.