"Canon" doesn't enter into the equation. The Pocket license doesn't say "adhere to canon." It says "you can do This, but you can't do That, and when you do This, you follow the guidelines we set.".
I have never in all my years of writing and editing tie-in books seen the word "canon" in any contract, licensing agreement, deal memo, or other legal document.
"Canon" is a fannish obsession. It has nothing to do with how licensing and merchandising deals actually work in the real world. Ditto for issues of narrative logic like "well, shouldn't there be a Prime Universe version of such-and-such?"
Mind you, I've never actually laid eyes on the STAR TREK/Pocket Books contract, but I've negotiated similar deals in my time. Trust me, "canon" never comes up.
