For me, every episode, book, comic, movie exists as a glimpse at an alternate universe. Some of them we have seen before and so they exist in the same universe. Others, show no obvious connection.
Was Khan a product of eugenics or genetic engineering? The answer is yes, depending on which universe we're watching.
Is there a 50 foot clone of Spock on the planet Phylos? Sure, just not in all universes.
Was Kirk a drunken frat boy or a stack of books with legs while at the Academy. Again, the answer is yes to both.
I much prefer the Klingons as depicted in The Final Reflection as opposed to the drunken, amoral biker gang we got in TNG/DS9. Does that mean that Ford's Klingons aren't real Klingons? Nope, they're just as real as any Klingon ever has been, which is to say, not at all. The same goes for Diane Duane's version of the Romulans as compared to the so called "official" version.
If the owners of Star Trek have allowed someone to legally publish or produce something with the name Star Trek on it, it counts. I'd even go so far as to include the fan films in that. If they're not issuing a cease and desist order then it's showing at least a degree of acceptance.
If something contradicts something that has come before I simply shift it to an alternate universe and carry on. Much easier to deal with than trying to wedge everything into one "prime" universe *Which is a dumb concept to begin with. It feels like we're back to imagining the Earth is the center of the universe.)