It's been standard operating procedure throughout the history of Trek tie-ins for different licensees' publications to present different continuities. This goes back as far as the '70s, when Gold Key Comics offered one version of McCoy's daughter and divorce history while Bantam's Planet of Judgment
offered another. In the '80s we had Pocket offering one version of Kirk's first mission on the Enterprise
within a year of DC offering a separate version. And to date we have at least seven different versions of the end of the 5-year mission: four from various Pocket continuities, one from each of DC's two TOS volumes, and one from IDW. And David Goodman's book Federation: The First 150 Years
handled the Romulan War/UFP-founding era differently than Pocket's novels (including my upcoming Rise of the Federation
) have done. Not to mention, of course, that Pocket and IDW both have more than one continuity apiece.
So the games doing things differently from Pocket or IDW is just par for the course. If anything, the exception to the rule is when one licensee does
reference anything from another.
Just yesterday I was looking over the Marvel Wiki, and they have this insanely huge list of alternate "Earth-###" realities, a different numbered universe for every alternate version of Marvel Comics continuity, from the mainstream comics to all the alternate worlds visited therein to every single issue of their What If?
comic to every movie and TV and video game adaptation ever done. So not only do you have Earth-616 for the main comics universe and Earth-1610 for Ultimate Marvel, but the Marvel Cinematic Universe is Earth-199999, the X-Men movies are Earth-10005, the '90s X-Men and Spider-Man cartoons are Earth-92131, the 1967 Spidey cartoon with the catchy theme song is Earth-6799, etc. No attempt to reconcile different tie-ins unless there's an explicit crossover -- they're just accepted as parallel tracks of the multiverse. (And no, I have no idea what the source is for those numbers or who came up with them or what system they use.)