A general point regarding the sets associated with shuttlecraft operations:
All the doorways and corridors depicted in the screencaps upthread seem to extend quite a bit beyond the outer walls of the shuttle facility that can be glimpsed through these doorways. That is, there's a lot of volume between the shuttle holding area and the outer walls of the starship. Now, if those doors and corridors are on the same level as the flight deck, this means the ship is more likely to be over than under thousand feet long...
...However, if they are on the same level as the hangar deck
, below the flight deck, then it is relatively simple to argue that the hangar deck is a compact space, not nearly as wide or tall as the flight deck. Plenty of corridors could then exist between the outer walls of the hangar and the outer walls of the ship, without a need to assume a larger ship.
If we want to squeeze the corridors on the same level as the flight deck, we probably have to install them at an angle other than perpendicular to ship centerline. That is, when "JtB" shows a corridor extending away from the shuttlebay, it need not extend to port or to starboard exactly - indeed, it cannot, not if the ship is under a thousand feet long. Rather, it might extend towards the bow of the ship at an acute angle, so that the doorway is set in the forward
wall of one of those pocket alcoves, and not in the side
wall of such an alcove. The alcoves do suffer from a notable lack of doors that would be visible in the side walls - whereas there does seem to exist a door in the canted forward wall of the longer alcove, at least in some model pics, even though the actual episodes never show this.
If we don't want to move the corridors to the deck below the flight deck, and don't want to use corridors at odd angles, then we probably have to position the "JtB" doorway at the unseen front wall of the flight deck. The flat greyness on the background would then be the inside of the space doors, and the shuttle would be rotated to face the port wall...