"it splinters from the previous timeline" pretty much covers it.
This does not equate to "it has no connection to the previous timeline whatsoever and so absolutely anything from prior canon can be thrown out".
Khan is from before the timelines diverge, it's as simple as that.
King Daniel Into Darkness wrote:
Just look at the dozens of ignorant cries of "Khan is a Sikh!" whenever Startrek.com posts a picture of Benedict Cumberbatch to hype the latest issue of the Khan prequel comic.
Speaking of which: