I think it was just different editorial philosophies, and maybe a function of the different formats. Comics tell ongoing, often serialized stories moving forward in time, so once they started out their series by tying into the latest movie, they naturally continued forward from there. And when DC first got their license, it was between TWOK and TSFS, so that was where they started from, and as they moved forward they stayed current with the movies. Novels, on the other hand, tell more self-contained stories, and at the time there was little continuity among novels. So although Pocket started out in its first year or so doing mostly novels set after TMP, it wasn't long before they started jumping around and doing 5-year mission stories, and that turned out to be the timeframe that most authors preferred working in. And there definitely wasn't an attempt at a single continuity between Pocket and DC. There were some cases of cross-referencing, like Diane Duane using her novel characters in the comics she wrote, but there were other cases of direct contradiction; for instance, Pocket and DC did incompatible versions of both the start and the end of the 5-year mission. I still count most of the Howard Weinstein issues from Vol. 2 in my personal continuity along with several of the novels from that era. Some other stuff in Vol. 2 has some conflicts with canon, though; for instance, the Peter David issues portray a 23rd-century Klingon emperor (contradicting TNG's "Rightful Heir"), and the Debt of Honor graphic novel offers an explanation of ridged vs. smooth Klingons that contradicts later canon. Also, there might be an issue reconciling the PAD issues of Vol. 2, which begin shortly after TFF and continue serially for some time thereafter, with In the Name of Honor, which mostly takes place in the month after TFF. Although it might be possible to fudge the timing a bit.