Naw, That's not soundstage bits, it's clearly a Jefferies style bit of set dressing. Honestly, I prefer the unaltered JTB footage, as we can assume that it's not the flight deck, but, rather, the hangar deck below. Which makes more "space ship architecture" sense. After all, if that's the flight deck, and we're seeing the upper gallery there above the shuttle, that means that Kirk and Spock are entering the bay from one of the sides. But the width of the ship really doesn't allow the flight deck we see to fit in the exterior we see if we also have broad side corridors. Having this be a lower hangar area means they could be entering from a door that is forward of the shuttle and the camera is looking aft, which makes more physical sense.
I prefer to think that the shuttle lands in the flight deck, rotates and lowers on the elevator to the shuttle hangar, which is smaller volume that gets sealed off from the flight deck (which is depressurized to space) and pressurizes more quickly, then the passengers disembark. I imagine all the boarding and deboarding of shuttles usually happens on the smaller hangar deck and then the shuttle rides to the elevator to the flight deck for launch every time.
--Alex