I would place the "Mark of Gideon" windows on deck 2 or 3, as the curved wall could be related to the superstructure just below the bridge dome. It's been a while since I watched the episode, but didn't Kirk and his girlfriend basically just tool around the primary hull? I recall scenes on the bridge, and in in his cabin, and in sickbay. Did they go down to engineering at any point? I can't remember. But anyway, deck 3 or so would allow a primary hull possibility.