I only proposed "director's intent" to help us rationalize the scene. The way I see it you can either have the doctor's office in "The Changeling" on the port and/or on the starboard side.
Of course, DP Herb Wallerstein might have watched Cg and decided he wanted to have room 5R 671 (new door sign?!) next to 5R 672 and therefore left the Cg area "untouched". In this case a later DP would have resolved the issue but that is, of course, pure speculation.
The chapel is a difficult issue, I presume there's only one aboard the ship and the one from "Balance of Terror" is essentially the same as in "The Tholian Web". I'd be inclined to prefer the one from "The Tholian Web" as the "leader" (briefing room set).
If we adopted the editing of "Balance of Terror" as the real thing, the alignment of the briefing room set would probably stick out like a sore thumb in the deck plans.