My understanding is that it's not so much that the novelisation is of the director's cut, but that the people writing them are typically working from (at best) the shooting script (and at worst, an earlier version of the script). The book needs to come out at around the same time as the movie, and there simply isn't enough time to re-edit it and print it after the final editing decisions are made. You'll frequently find sections in the book version that only end up on-screen as a director's cut or in deleted scenes, and sometimes just never at all.