I was kind of surprised they didn't have anything on the covers of this year's TOS novels to let people know that it was a TOS novel, not a Abramsverse novel.
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.