I don't think it's about in-universe timelines. Big corporations and legal departments don't think in those terms.
I recently read the CBS' rules for Star Trek fan films (a completely different beast to licenced novels, but bear with me), and one of them was that NOTHING originating from JJ Abrams' rebooted Trek is to be mentioned or seen - and an offhand comment about George Kirk's time on the USS Kelvin was cited as an example of what would get a fan film pulled.
The novels obviously don't have such a strict policy (unless the little references we've had to the movie thus far are really "getting stuff under the radar"), but I strongly suspect that Pocket were told to lay off JJ's movie concepts, not just his alt-history.
Of course, I may be totally wrong and Pocket are just biding their time until we're closer to 2387 in-universe, when we'll get loads of stories centred on Red Matter, squiggly Vulcan ships, transwarp beaming and the supernova.