Is it possible that these other portholes aren't quite placed in the same way on the full 8' shooting miniature?
Possible, but not the case in this, well, case.
Perhaps there's something to the mechanism of that door prop that absolutely calls for it to be mounted at least a couple of feet above studio floor level, and this particular area was designed to facilitate a shot of the doors from the inside, one that was never needed in the end? (Note that the door is above studio floor level in ST2, too, adjoining the torpedo set with the torp track ditch under the set floor...) Perhaps the set depicting the bridge docking port was to be reused without modifications, regardless of the reasons of having those steps on that set?
Nothing about the secondary hull was done quite to Probert's liking, but was dictated from on high; perhaps the exterior reflects his original ideas that never could be implemented in full?