I agree. I have never, ever, ever understood folks who fight against the possibility/likelihood that Chekov was serving on the Enterprise during Space Seed, but simply was not shown onscreen in the episode. Simplest, most obvious explanation. We don't assume that every moment experienced by all 400+ humans in the two vessels was shown onscreen, and that all these moments starting with the discovery of the Botany Bay and ending with Khan's transport to the surface of Ceti Alpha V took place in less than 1 hour! I am forced to assume that some fans must also believe that toilets do not exist on Constitution class starships because they have never been shown onscreen.
When I watch an episode of Law & Order SVU that focuses primarily on Elliot and Olivia, I don't assume that lack of an appearance by John Munch means that the detective was transferred to a different precinct. Or was eaten by wolves.
Actually, the bathroom scene where Khan and Chekov shared an awkward, uncomfortable silence at the urinals on Deck 5 was cut by the censors, due to network sensibilities of the 1960s!