It's been an alternate parallel universe ever since Tasha Yar went back in time with the Enterprise C, ended up being captured by Romulans, and had a half-Romular daughter who went on have her own warbird in the fleet; the ship was supposed to be destroyed with all hands and it was definitely not. Hell, it's been an alternate timeline since Kirk went back to San Francisco if you want to get technical. Which means it's actually been an alternate timeline since the eighties. And that's not even counting the stable time loop involving the 19th century and whatnot.
The Trek timeline is a convoluted knot. Why should the latest movies be any different in that respect?