This conversation reminds me of a recent conversation I had with my friend about the show Enterprise. He said he decided not to watch it because it bothered him that a series set before TOS, would have technology that seemed more advanced that what Kirk and crew are using later.
He didnt like what the writers were attempting, in showing a closer to realistic look at where Star Trek future would be from present day based on the technology of the day.
The error in his logic is that the show in no way is saying that the tech Kirk and crew use later is less advanced than Archers. This is an area where as the viewer you have to look through shutters to a degree. It all comes down to the production of the show and the year it was produced.
Things available in 2000 are obviously more advanced that what was on hand in the 60s. You have to choose to not look at how outdated a device is on Enterprise because in the world of Star Trek its further advanced that what is being used on Archer's Enterprise even if aesthetically it looks more advanced.
How the viewer or reader chooses to approach the material is going to affect the experience.
Watching the new movies, it establishes that Spock goes to a parallel universe. So logically as long as we dont see Spock around in the books after a certain point, there should be no continuity glitches. That said, seeing how the Star Trek universe unfolds in the movies, ideas might appeal to the writers of the books and being applied, in most cases getting from point a to b isnt as important as whats at b when you get there as long as your not sidetracking to x along the way which only confuses things.
An example of what I mean is the whole thing about the Klingons.
As funny as the scene with Worf where he is confronting about the TOS Klingons being so different and him saying "We dont talk about it" that scene was frustrating to a degree because until that moment you just accepted that by the time the Motion Picture came around the budget was bigger so the Klingons got to look cooler. Now though because it was acknowledged in universe there had to be an explanation.
There has to be a line where you just enjoy whats there and not overthink it.
If nu universe elements creep into the prime novels, as long as the story is well written and the characters are true to whats established or changing in a story structure I think the reader needs to just go with it.
Im not trying to tell people what to do but I do feel that in the case of my friend, it can be detrimental to enjoying what you like, as he wont watch Enterprise, which is his perogative but I feel is for the wrong reasons.
I'll stop rambeling now...