depite subsequent canon rendering so much of the novel irreconcilable with the current Trek universe
With a book this good, one is motivated to make the effort to reconcile anyway.
What is contradictory there? Due to ENT, transporters appear earlier on, and so does dilithium - but as with cloaks, we could plead "rat race" and argue that the things introduced in the novel were new iterations with superior qualities. Say, naturally mined dilithium might be a galaxy-shaking development, as opposed to the never-seen, never-described substance of ENT, if we assumed the latter was an industrial product with an annual global yield of micrograms...
Klingon ideas on when first contact happened are already indicated to be different from (what the Klingons know of) human ideas - both
could be written down as creative rewriting of history, something the Klingons are quite famous of in both interpretations.
The canon and novel descriptions of the Klingon culture and biology don't appear to overlap sufficiently to create contradictions. We never saw the lack
of Games, Thought Admirals, orphanages, Name changes or Fusions in canon Trek! Nor was there in this novel an explicit lack
of those Klingon features introduced in TNG or DS9 or VOY. Or was there?
As for the relative ages of Spock and this young Leonard McCoy we never see... Perhaps the good Doctor had a cousin who was a namesake?