Whereas I'm willing to write it off this time because really only people who have actually seen Space Seed would be aware of it and they used MAYBE in that one episode and said description was from Marla "How the hell did she even graduate Starfleet Academy let alone get assigned to the Enterprise?" McGivers, so its not really an incontrovertible fact here it was speculation.
I don't know what you're referring to here. Spock Prime named him in the film as Khan Noonien Singh. So that's not a reference to "Space Seed." The character's full name, with a Sikh surname, is something that was established within the film itself.
Besides the Space Seed 1990s had all sorts of major differences with the regular 1990s, so who else knows what other differences they had.
Again: the difference between Trek continuity and reality is irrelevant to the question of how two different branches of fictional Trek continuity relate to each other
. We know for a fact that the Primeverse and the Abramsverse diverged from each other as a result of Nero's incursion. That is the whole underlying assumption of the movie continuity: that it's the same universe as Prime until 2233. This was reaffirmed in the scene in the film where we saw models of a number of previously established canonical ships, including the ringship Enterprise
, the Phoenix
, and NX-01, on Admiral Marcus's desk.
So we know this Khan has to be the same individual we met in "Space Seed," and that he lived exactly the same life prior to his exile. The only difference is that in the new timeline, the Botany Bay
was found a decade earlier by Section 31.