As far as the novels go, there are too many contradictory stories going on. How many different fates for the Romulan Commander from "The Enterprise Incident" have been published? Not fanfic, but officially licensed novels from either Bantam or Pocket? Or backstories for any of the characters? It was just simpler to lob off all of the novels, even Roddenberry's own TMP novelization, than to sort through the literally hundreds of novels and try to pick and choose which one fits, which one is rubbish, etc. And don't even get me started on the various comic books.
And note that Jeri Taylor's Voyager novels ceased to be canon once she left the show.
It's really a very simple rule: Only what made it onscreen counts. And for the writers, don't contradict what came before, with the proviso for the more advanced players, unless you can come up with a really compelling reason to make the previous writer a liar, or you can figure out a way around what came before so that it really isn't a contradiction. And it's really not any more demanding than any other show, so I don't see what the big problem is in sticking to the established record.
Where it gets dicey is when you start trying to toss out stuff that was actually onscreen, which is apparently what was going on when Richard Arnold was doing his master's bidding, and apparently got a little carried away. As has been discussed elsewhere, TAS was never actually decanonized, just put off limits for a while due to the legal issues of the shutdown of Filmation. Once that was resolved, the TAS references came flowing in. As for dumping the third season of TOS and every movie except
TMP, I don't think anyone took that seriously, even Roddenberry.
And as far as TFF goes, I still like the notion that the whole thing was a drunken ghost story told around the campfire. It would certainly explain certain bizzare aspects of the story.