The One Bay Option could allow for what we see in the movie so that beyond the inner tube doors the route splits into the tube one and two. I believe that's one of your options you've pointed out.
Diamond Joe. I disagree with your position on moving the Engineering Section.
Engineering is exactly at the juction between the Neck and the PTS and of Course directly bellow the deflection crystal of the impuse engines. Engineering as to be where it is.
In my opinion the most important thing isn't what we see in the Movie. It's the Plans themselves. Unless you're truely forced to change things because of an error in the design (Which happens all the time with 2D schematics ) then leave it alone. The designs were made in retrospective to other elements that aren't immediately seen. If you start changing things that are superflous just for how they look it may screw you in the end.
Like my guys say: Cut to fit/Paint to Match