About the Shatnerverse and regular TrekLit: I’m not so sure there is much in the way of irreconcilable contradictions between them (although I haven’t read everything, I think the biggest problem spot is the mirror universe) – I always thought of it more as they just never EVER mention that Kirk is up and about in the 24th century in any of the other books.
There are major contradictions between the Totality trilogy (the Captain's _____
books) and the main novel continuity (hereinafter MNC). In the Shatnerverse, Bajor is not yet a UFP member in 2378, while in the MNC it joined in 2376. The Shatnerverse starship Titan
spends 2380 participating in Romulan reconstruction post-Nemesis
and doesn't have its first encounter with a new alien species until 2381, whereas the MNC Titan
spends much less time at Romulus and has its initial first contact in March 2380. The Shatnerverse Doctor/EMH is in the Alpha Quadrant in mid-2381, whereas the MNC Doctor is aboard the Galen
in the Delta Quadrant at the time. Most significantly, the Shatnerverse Kathryn Janeway is still alive and well in 2381, a year after her death in the MNC.