Then again, that's the same reason why there are no window matches to "The Conscience of the King". The windows at the back of the secondary hull are rectangular when they need to be square to match up. For the purposes of my project, these windows are there but normally shuttered and thus blended into the hull.
The problem with this approach is that you then have to explain why the windows which we know are ACTUALLY IN THAT LOCATION are not visible in the episode.
It's easier, and more logical, to treat this as what it is... a small production "snafu"... and that the windows seen there are intended to be the same windows seen on the model. After all, it's not very likely the the Enterprise's auditorium, gymnasium, and even a starbase's computer center are built in rooms which are identical to the Enterprise's engine room, is it?
If you focus too much on the small mismatch in window shape, and ignore the clear INTENT that these two windows seen there are intended to be the same two windows seen in that location on the hull exterior... you're going too far, IMHO. Then again... I'd never dream of making the Enterprise into an "Autobot" either... sooo...
The "Mark of Gideon" could be matched up to the curve of the secondary hull, but again it might go to a window not normally visible in external shots when shuttered.
and
And I expect that the window we see in "Gideon" is in the dorsal... probably the starboard side (port shown here, by the way), second row from the top, near the aft edge of the dorsal:
I don't think it would work for the neck as the scene shows a curvature to the wall suggesting somewhere in the secondary hull while the neck is vertical. (You are looking at the posted reference shots, right?)
Except that, of course, the hull there isn't "vertical" as you seem to be thinking. I chose that particular spot for a reason, you see. There is a gentle curvature which very nearly perfectly matches the on-screen shot in the specific location I mentioned. there is no other place on the ship that matches it quite so well, though it's true that there are a couple of secondary hull spots which come reasonably close as well.
If I'd suggested one of the windows further forward, they would be nearly vertical. And if I chose one of the ones way forward in this region, they'd be on an outwards-sloping section of wall... as you can see here, for example. You're looking forwards, by the way. Most of the windows are mainly vertical, but notice the ones most to the front.
Now, there are two places where I think that this shot would be likely to have taken place, both in the dorsal. Either the aftmost room on the second deck in the dorsal (which I refer to as deck 9D) or the fourth one down (deck 11D). In MY model it would have to be on 11D, because I've got a Jefferies tube structure and the entire dorsal keel in the region aft of the window on 9D, but you wouldn't HAVE to do that.
On either location, the window will be in a section of hull which slopes slightly outwards as it goes from the ceiling to the floor. It will not be a "parallel" slope, of course... but it works remarkably well in either location, I think.
I just like the idea of those rooms in the dorsal being INTENDED for "recreational relaxation" purposes, and thus would be the most likely spot for Kirk (or anyone else) to go in order to stargaze.