Getting back to work on this, and going back to the near-literal "needle" idea, focusing on the exterior components. (I'd forgotten about the revision until looking at this page of the thread again!)
As for the "where to eat" angle, I'm thinking "wherever they please, so long as it doesn't mess up operations". So, lounge and living quarters and maybe in the cargo hold(s), but not in the cockpit, the engineering alcove or the lab space.
Nice to see this again!
I'd imagine there would be numerous sliding- and folding fixtures in order to keep common areas as multipurpose as possible, or just clear of clutter when not in use. Fold-down table, slide-out additional seating and countertops, etc., as in present-day boats and RVs.
However, I do see the point about keeping it separate from the medical bay, or at least arranged so that the medical portion can be partitioned off when in use.