It can't be the observation deck in the original shot. For one thing the things that one might think are the bottom of the windows are far too low. And in both the original and TOS-R the observation level looks too far away--the perspective is too exaggerated.Phantom - there is undoubtedly something up there in the original footage, but it certainly isn't a section of the observation gallery!
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Looks like a section of the lighting rig, maybe? The camera certainly never focuses on it for more than a fraction of a second, so I'm pretty sure it was not supposed to be a part of the set.
Conversely, the opservation gallery that was added by TOS-R was very much supposed to be seen:
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It's just a shame that a sideways entrance to the Flight Deck is both impossible on a 947' Enterprise and completely at odds with the landing deck as depicted in both TOS and TOS-R.
Also, the CGI observation gallery drops in height for some reason in between episodes...
And the simple fact--as you've affirmed--having the corridor and access door on the side of the flight deck is impossible.
It's simply one of those things that was unfortunately messed up both originally and in TOS-R. It's more inexcusable in TOS-R because it's something they should have realized and simply showed the hangar deck doors in background of the shuttlecraft. Then the shot would make sense. Or they should have just left it alone.