Yes, it does seem strange but this could also be a 'Usual Suspects' moment. Just because we have knowledge to contradict Khan doesn't mean the characters do I suppose.
I think that the characters could certainly be expected to have enough knowledge of history to know whether there was a global nuclear war in the 1990s. That's not exactly the sort of thing that would be overlooked in history class.
Or of course proof that (IDW) Nero did not come from the Prime Universe.
It's simply proof that the comics are non-canonical. It's not the first time that they've had some strange interpretations, some of which have clashed with the Bad Robot movies as well as with Prime continuity.
This is why tie-ins are not canonical as a rule -- because even with an ongoing attempt at oversight, it's hard for film or TV producers to maintain really solid continuity in tie-ins created by other people while the producers themselves are busy creating the canonical work itself. Generally the only times it can work are after the canon series has ended and the creators are able to oversee the tie-ins more directly -- which is why the Babylon 5
books written after the series ended are canonical and the books written during the series are not, and why the Buffy
comics written after the series are canonical and the books and comics written during the series are not.