It's certainly not impossible that it was all a parallel reality even before Nero and Spock travelled back, but that does somewhat rob it of a connection to what came before from a dramatic standpoint, and would seem to be counterindicated by Nimoy being credited as "Spock Prime."
I would prefer to look at the casting of Cumberbatch as you-know-who [don't read further if you don't want the surprise spoiled!] as akin to the Robin Curtis vs. Kirstie Alley as Saavik thing mentioned above: just a different actor playing the role and not an "in universe" difference. It's not as if a character who has been genetically engineered must be clearly of one particular race, nor must an actor's race or appearance be seen as directly reflective of a character's. (After all, Montalban was not a Sikh either, and moreover the character's designation as one in "Space Seed" was only McGivers' guess
to begin with.) The issue of his race doesn't come up at all in the new movie, and is irrelevant to the story.