The problem is we don't really know where they're disembarking from--the filght deck or the service deck. All we see is an open area with no discernible details (certainly none remotely resembling the flight deck).I was under the impression, based on the positioning of the shuttlecraft, that they were to one side.
*EDIT* I just rewatched the shuttle landing from JtB again, and yes, the entry IS from the starboard side of the hangar deck.
Also the miniature set shows there are no such doors on either side of the flight deck. If the shuttlecraft were oriented at right angle to the ship's centreline then maybe a door could be in the centre of the forward wall. But then what's forward of that wall. A lot of conventional thought is the Engineering section.
However, if the craft goes down to the service deck (for whatever reason) and turns at right angle to the centreline then the view from the service deck's entrance might be similar enough to what we see onscreen--again overlooking that the area has no detail onscreen.