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!
Sure, we could argue that Auxiliary Control isn't in fact a Room but a maze of rooms, but even in that case our heroes seem inexplicably lost. 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.