Admittedly, I have only read a few pages of this thread, but the idea that the sets filmed for TOS do not match the exact "in-universe" dimensions of the ship, and therefore those rooms would fit into the ship if they were sized, and more importantly, shaped, a bit differently, seems to resolve, for me, almost any issues with the size of the ship in TOS.
When TOS was made, even a movie taking place on a real naval vessel would have had sets that were shaped or sized a bit differently for ease of filming, but today with film crews able to use smaller equipment, those sets would be able to be adjusted in size and shape to fit at 289 meter ship. Every official source prior to 2009 that I have seen, if it gives a size, gives that size, or something close to that in feet.
The "problem" is that the new shows did not try to create sets that were these "altered" versions of the original sets that would have looked like, and had proportions like the rooms would "in-universe." Instead they made new sets. They could have gone farther to make it look like the original and yet added detail for without changing the details that were already visible in TOS. That would have satisfied two groups: those who wanted to see a show in the era just before TOS look like TOS, and those who felt that the look needed updating for newer-style TV's. But they went with their own different look, which in my opinion opens them up to the argument that this is not the same universe.
I don't consider anything made after 2009 to be canon to what came before, so what I called a "problem" in the above paragraph is not actually a "problem" for me, because I don't feel the need to make the first two eras of production fit with the later eras.
that contain no crew spaces
We actually don't know that they don't contain crew spaces. Admittedly, Jefferies intended the engines to be "dangerous." However, after there has been a Nacelle Control Room in TNG, and given that the locaiton of the engine room is not clear anyway, there could be rooms in the forward part between the Bussard scoop and the vents, just above the struts. In TAS, they drop a living anti-matter item into the engine, and that could have been in the nacelle, or it could have been just below the plasma transfer conduits. The nacelles could be sometimes able to have living humans inside, and sometimes not, or always have habitable portions, or never be able to accommodate living humans.