I think we all agree that nothing really fits. Concept Drawings do not equate to Exterior Models do not equate to Interior Sets, and vice versa.
@blssdwlf uses a 22' shuttle in a 1084' ship, and
it looks great! 
For me, trying to stuff a 24' shuttle (Kirk dialog) into a 947' ship (viewer graphic) with the entire hangar bay behind the pylon looks like crap with a lot of compromises. (I wonder where the script writer got the 24' dimension for a shuttle?) Oh well, that's my ship conditions at this point.

Image matching the hangar model using a 24' shuttle, the ship would balloon to 1120' or larger. Angling the observation deck to run parallel with hull was an option (Shaw did that), but IMHO, it's ascetics are not as good than straight interior hangar walls giving the flaring observation deck corridor.
Square windows into round portholes? Meh. I think the two adjacent square windows from the interior set could represent one large rectangle window on the hull exterior; the interior framing (or anything inside the ship) are not seen from the outside. Or the intent of the set designer was to capture the dual windows seen in the aft hangar bay on the external hull, but it's execution was less than perfect.
As for the COTK location of the observation deck, when Lenore looks down, I assume she is seeing the big yellow circle in a big red square, probably with a shuttlecraft sitting on it. It's most logical that she is viewing out of one the hangar model established windows. COTK was production order 13, while the Galileo Seven was order 14, so, I assume the model was finished by COTK (maybe film in the can was still working for TGS).
KIRK: This is the observation deck. That's the flight deck down there with the shuttle craft.
If this is the case, would you put a red security fence/gate to restrict access to the high value control booth (starboard side location), or put the gate to restrict access back into the general ship (port side location)? I would keep unauthorized personnel out of the control booth where, with a push of a button, you can evacuate the air in the bay, spin the shuttle, drop the elevator, or possibly open the hangar doors to space with personnel in the bay. This layout would fit even better in a bigger ship.