As far as I can tell, the set diameter and bridge dome are 'close enough for government work'. The exact measurements may be off but we have to remember this is a Hollywood production, and not a group of engineers making a real starship. They're not going to get the details exact, ever, and it's really kinda stupid of us to expect them to. The importance was making the show, after all, not satisfying nitpickers 40 years from now.
Agreed from a personal viewpoint. From what I remember of people who have made a more detailed study, whose reconstruction of the 11' model has a bearing on how "off" the fit with the sets is. 90% of Treknology is nitpicking though, right?

On the other hand, if they are in disagreement, we all probably want to be informed of the details before we go off half-cocked. Its the difference between purposefully ignoring a fact and being utterly ignorant of it.
Personally, I would probably slightly modify the bridge dome to address issues, but it may not be that simple. The other alternative is to slightly 'massage' the bridge floor plan until it fits, which is somewhat less satisfactory. Either strategy will likely result in calls of 'heresy' from competing camps based on what they consider more sacrosanct (the model or the set). For myself, I'm a practical man, and I'm all for a compromise that gets us closest to both 'representations' of 1701 (interior and exterior) being 'nearly' accurate and working for a 'real world' ship. Other people will have differing agendas.
But ultimately, the conflict between the model and the sets (and the description & 'plans', inadequate and contradictory though they are) will only rear its ugly head in a few choice locations. Reasonable changes to either (or both) will resolve the problem, but the result is conflicting, slightly different, and oddly personal conceptions of the ship for which people will fight to the death. To which I say, "Can't we all get along?"
Personally I've taken the view that, as Hollywood actually did, the lift and station immediate starboard were swapped for dramatic reasons. Solves all the issues neatly. If that's too much, the other obvious solution is to correct the location of the lift housing on the model itself, sliding it to port a little bit. (I've been tempted to do this on my Jaynz models, just to see if anyone would notice.)
My
own perspective is that, while it is true the 'inline' orientation was changed largely for cinematic reasons, what we see on screen for the turbolift is the orienting feature of the bridge set and the turbolift shaft on the model shows us how it relates to the rest of the ship, thus the bridge is... rotated. A simple (and elegant) solution for a simple man.

With sensors, artificial gravity and inertial dampeners the bridge could be upside down and backwards and it wouldn't make any difference to what we see onscreen, so a little rotation so the Captain can keep an idea of who is sneaking onto his bridge late for their shift is alright by me.
But others disagree, and have their reasons. IDIC.
Amusingly, the deck heights shown in the ship diagrams match the hard line on the walls just above the doors. We can pretend that anything above that 'on the sets' are actually not really there.
Sorry, which diagrams? TMoST, BoGP...?
Speculating blindly... I suppose its entirely possible that the inter-deck spacing consists only of a deck plate of around an inch or so... I've assumed about a foot to allow the running of conduits and what-not, but that is an assumption. For what its worth... It could be a combination of both, with some decks having thick protective or 'conduited' bulkheads and the remainder being relatively thin and functional.
One needs to ascertain exactly how big the bridge set is. Do you accept the likely 9/10ths scale it may have been built at as the "real" size or do you try determine how big a real bridge would be? Then how is it supposed to fit under the dome atop the saucer hull. And finally remember you're trying to fashion a "real" ship and not just one of plywood sets and plywood hulls. That means you've got to include likely mechanicals for such a ship and a believable hull structure.
My understanding is that the bridge was built 1:1 and the "real" size of the ship was downsized about 10-13%, so my
speculation would be the bridge ended up being unintentionally "over scale". Are there plans showing an oversize Bridge (I think FJ and FASA had such, but I assumed those were an error followed by... excessive borrowing)??? Which is I think the opposite of what you were saying. I think I'm misunderstanding you here, and you are actually suggesting an under-scale bridge that conflicts with the studio model... However, I reserve the right to be
absolutely wrong.
I think people have researched the Bridge's scale, but my recent drive crashes haven't helped my access to archived information. I would love to hear discussion from more of the researchers on their findings: i.e., a 'state of the bridge' report on the subject from all 'department heads' so to speak. Even in its own thread.
^^ I rather liked how FJ had a service space between the bridge and the outer hull. It doesn't have to be exactly like that, but I don't see the bulkhead just behind the stations as being the outer hull. I see it more credible if there's "stuff" between the inner bulkhead behind the consoles and the outer hull.
It creates a double hull, which obviously is more battle-rugged. Clever man that 'militaristic' FJ.
Of course, when they've blown out a TNG Bridge wall (Nemesis only?) I don't remember it having a visible exterior area. Not that I have paid that much attention.
My memory fails me, but I think someone here had the viewscreen up front, the turboshaft directly aft, and explained it all by having a ring for extra turbolift cars surrounding the bridge to either side--so the car would come up to the bridge, then swing around it. The top of that bump perhaps linking to a larger station just above or maybe another ship...
My personal opinion is that while the the topic is related to the bridge size/location, going there opens a different can of worms, and we already have a large one open. In short, it deserves its own thread (and I would guess there is no shortage of them looking into the past). "Nothing is new under the sun" is a Treknological proverb also... or so it seems. To summarize, while sinking the bridge generally vaporizes all bridge 'fitment' issues it also allows you to do almost anything else you would like... as long as you don't mind sacrificing more internal volume to simply service the bridge 'support systems'.
As long as 'we' can't decided on the definitive size of the ship other than to say that its somewhere between 940m and 1080m its not clear that the 'Bridge Sinkers' have a dog in the fight.
If we fix on a size of the ship, and
if we decide on a 'correct' reconstruction of the shape/size of the bridge dome on the 11' model, and
if we then find one doesn't fit in the other, and
if one rules out modifying the layout of either to accommodate the other,
then there is a empirical argument based on the topic of this thread for sinking the bridge. I'm not saying all this work hasn't been done, its just that its taking us more than a bit off the beaten path (for this thread) to look into it all again.
Or, to put it another way, this approach largely invalidates the one we are discussing. The first approach is an attempt to estimate the size of the ship based on fitment of the Bridge module (or the lack there of) and subsequent 'upscaling' of the ship to make a fit. In contrast, 'sinking' the Bridge more or less eradicates the fitment issues (if they exist), and therefore invalidates the scale comparison attempt.
BTW, the weather (and consequently the roads) isn't exactly great here so I'm likely to be dropping in and out of the discussion from time to time (there's no useful internet off the beaten track where I live, so since broadband won't come to me I have to go to it).