Leaving aside the square/rectangular designer's intent controversy for a moment, when I did my first ever Thermian-style design back in college, it turned out that the 2 windows which were meant to correspond to the observation deck were actually too low down to be anywhere near it, hence I went for the "shuttered" approach to the windows, the same as blssdwlf
However, that's for a standard 947' vessel.
If the Enterprise were actually closer to 1500 feet in length (as suggested by an earlier post when fitting the shuttlebay set into it), maybe that is no longer the case, so the rectangular windows could just be further on down the corridor!
There are a ton of issues with the 947' length... a big part of why my ship isn't 947' is that the ship simply didn't work at that length (I initially tried). Of course, 1080' is much closer but there were still some issues that didn't quite work with that. I eventually arrived at 1067' as you may recall. This was driven by a bunch of "spacing" issues, not the least of which was trying to get windows to line up properly with deckplanes.
In my version, the landing bay observation gallery is literally on the same deck plane as the rest of that deck, and the windows match up very closely.
If you stick with 947' the problems are pretty severe, however.