To begin with, there's clearly a rear wall missing. The rear-facing computer consoles suggest one, but all I've provided beyond them is a sort of fence preventing figures from falling off the back of the Command Level. I would imagine that, from the outside, this wall would be heavily plated and might contain exhausts for climate control units. From the inside, this wall would be relatively nondescript and would contain no balconies/work stations because the entire station is designed for the captain to be able to look up and see what's going on with his own eyes (as well as for people on other levels to be able to see who's running the fortress). Anything on the rear wall would be out of the captain's sight lines and might even impede upon his ability to see the rest of the higher levels.
Believe it or not, there's nothing missing from the engineering level. Once again, a sight line must be maintained with the captain, so the catwalk would not continue against the missing back wall (outside of the captain's view).
The missing walls for the second and third floor wing rooms should be self-evident. These are rectangular rooms, intended to have four walls.
The third floor research facility deck might extend back a few inches further than it does here (the doctor looks like he's going to fall off the level), but I imagine a plexiglass wall right behind his chair, cutting off the level and providing a sight line to the captain.
The mess hall is the one wing room that I envision not being closed on all sides. I think it would not have an interior wall so that it could provide a pleasing bird's eye view of the station.
The White Room would certainly have a wall separating it from the research facility in order to provide a quiet, serene atmosphere.
The Transporter Core is, perhaps, the level that is missing the most for the sake of play space. I envision this level extending all the way to the rear of the fortress since it is not generally a manned station that the Captain would need to see, and also since it is too high up for him to see from his chair anyway. I imagine the remaining space would be filled with storage containers, some for storing energy from matter disintegration, and most storing basic building block elements like carbon and hydrogen for the replicator systems.
Of course, the final missing section is the remainder of the roof. I imagine this being covered largely with additional anti-aircraft weapons. The sides might contain additional windows to help light the interior naturally. The landing pads on the sides might extend back slightly farther as well.