That would depend on how one looks at that episode.
Is that episode part of the same continuity as the rest of the TOS episodes?
The "James R. Kirk" originates from Gary Mitchell, not Kirk himself from an in-universe POV.
How trustworthy is Mitchell in this case? Was it a deliberate mocking of Kirk or are they on a slightly different continuity than the rest of the TOS series or was it a mistake? If it was a mistake, that again points back to Mitchell's mistake although it would appear that it was deliberate mocking, IMO.
As to Deck 12, AFAIK, there are no references or indications in the TOS series as to where it is on the ship.