Having now finished the Trekmovie podcast interview, it does reveal that they had an explanation for the Ceti Alpha V/VI misunderstanding in Wrath of Khan built in, but that they couldn't find any way to insert it in without feeling like it stopped the story (and was too visual a concept, so they dropped it). The explanation given was a valid one- my only suggestion in light of that is that perhaps the reference raising the question should also have been dropped from the script, because currently Dr. Lear calls it out but the story doesn't include the answer to her question, so it just draws more attention to the unanswered issue.
At the same time, someone (I think it was David Mack? But I couldn't tell on the quality of the speaker I was listening to) said that he assumed that Chekov was probably under an NDA, or that the whole thing was classified. So for those that have had an issue with or question about the whole issue of Kirk's classified records, there's another clue as to what the authors were going for there.
Putting the pieces together, it really does seem like the idea is that Kirk reported this incident to Starfleet, but Starfleet swore them all to secrecy over it, a la Discovery season 2? In which case of course it would be interesting why Starfleet never followed up on this or went and decided to extradite Khan or put any kind of surveillance in orbit or do any kind of follow-up themselves...
Kristen Beyer acknowledged that people seemed to want to know why the logs were classified, and she thought that idea was unimportant and was pretty dismissive of the fan sentiment. Her opinion was that somethings had been classified beforehand, and then afterward when Kirk died, everything from his logs just automatically became classified because that is what Star fleet does when captains die. (???)
Regardless, that seems to suggest that Dr. Lear simply started her research a bit too late, and before Generations, maybe less would have been classified from Kirk's logs than currently is. (Maybe the thinking is that because there are a lot of people that still have harsh feelings toward Khan Noonien-Singh and the Augments, at least that part of the record was classified so that no one would know where he ended up and try and go exact vengeance, or the like? Based on Strange New Worlds canon and the bigotry they've added against Augments into the Star Trek universe, that does seem like a rational fear.)
So maybe the concept is that following Space Seed, the records did reflect that Khan Noonien-Singh and his followers had been found, but the pertinent details as to what happened to them, which might allow anyone with an axe to grind to extrapolate where they had been dropped off (since again, that was an unprotected, unpatrolled area for no apparent reason, given all that canon has built up around the concept by this point) were kept secret to protect Khan and the Augments (again, rather than any kind of active observation of patrol that would also serve to keep tabs on them...) This would either assume that Starfleet has a very low opinion of its officers, or that they expect unclassified Starfleet logs to just be open to the general public. So there are still holes in the theory. But it, at least, makes a bit of sense with the reference to 'Chekov and an NDA' and all of that. Even if the automatic classification of logs for the dead part is still a head-scratcher, and the concept of Starfleet both classifying the logs because they are in some way concerned with the Augments, and ignoring Ceti Alpha V, seem mutually exclusive to one-another.
Anyhow, just some further hints as to author intentions gleaned from the podcast interview.