They do show Leonard Nimoy as Spock, not Quinto so I consider that a hint. Yeah, I know Nimoy was in the movie but he's not the star and I seriously doubt Abramsverse novels are going to be advertised with Nimoy as the only character on the cover.
Why would they want to do that? The whole point of cross-promotion is to get people interested in one work based on its similarity to another work, not ward them off by dwelling on its differences. The fact that they're in different continuities doesn't matter from a promotional standpoint, or indeed to the majority of readers/viewers. The dedicated fans may worry about what stories happened in which reality, but casual fans just want more adventures with the characters they like, and don't worry that much about how they fit together. My X-Men and Spider-Man novels for Pocket were both timed to be promotional tie-ins to the movies, but they were both set in the comics continuity instead.
Ditto for my Fantastic Four novel. Technically, it was set in the comic continuity, but I always had the movie audience in mind when I was writing it. I wanted the book to be accessible to the casual reader who might be more familiar with the movies than the comics. And, yes, it was no coincidence that the book was published to coincide with one of the FF movies . . ..
^Right... I was told to put them in the comics continuity but write them like movies, i.e. as standalone, accessible adventures. Although my Spidey novel ended up being pretty closely tied to the comics continuity and was in fact a sequel to a comics story from the early 2000s -- but nowhere near as much as Jim Butcher's Spidey novel The Darkest Hours from the same line was a direct sequel to J. Michael Straczynski's first Amazing Spider-Man storyline. I made sure to explain everything clearly enough for the novice reader, though.
There were challenges, of course, like the fact that Reed and Sue have two kids in the comics, but not in the movies. I dealt with this by writing the kids out of the book as fast as humanly possible . . . as in a few pages into Chapter One!