Well, there is the fact that anybody who commands a starship is referred to as "captain," regardless of their actual rank.
Tell that to the people who wrote the second through fourth movies, in which Kirk was consistently called "Admiral" even when he was in command of a starship. Canonical Trek has almost never acknowledged that tradition (except in a few DS9 episodes), presumably because it would confuse audience members who were unfamiliar with naval conventions.
Anyway, it's a moot point. Regardless of his title, Kirk is portrayed in the novel as the regular commanding officer of the ship and has his entire standard command crew serving under him, including Spock. The only time those things could be the case after he starts wearing glasses in TWOK would be following TVH.
The problem with this idea, though, is that Spock is addressed in the novel as "Mr. Spock" rather than "Captain Spock." So the chronology of the novel is a bit confused. The glasses reference may simply be a continuity error.