Also, the interior sets were the same.
Their layout was not, though - not in plot terms.
That is, our heroes head for Auxiliary Control Room to read the logs of the Constellation
- and they almost walk past
the relevant door!
After all, the very room they walk past, the one with Decker in there, is also the one where they finally are able to access the logs.
Either Decker's ship is of a different design internally than Kirk's to begin with, or then all starships undergo constant modifications to stay up to date, and since these are performed at different times, the results are different as well.
Kirk wasn't walking past Aux Control, he was heading into the next area, where Washburn did his work. He only stopped when he saw Decker hunched over at the main control station.
Could very well have been that Kirk was going in the other room and could either access the logs from there, or he and Scotty would have split up.
You're the guy who comes up with a maze of "outs" to excuse stuff, why not this time?