As a fan of Enterprise: The First Adventure and Strangers From the Sky, that's my headcanon. McCoy was CMO, but on leave at the time of "Where No Man..."
I've read fan timelines which say "Where No Man..." was a pre-5ym adventure (not unlike Nibiru in Star Trek Into Darkness), explaining the different staff, roles, uniforms and ship design. But then I also like Q-Squared, which explained it as being one of the 4 alternate timelines in that book (hence James R. Kirk)
There have also been several novels where Kirk and McCoy meet at Starfleet Academy (also in the Kelvinverse reboot), so that's kind of etched into my brain. I'm sure Strange New Worlds will give us another version of the TOS crew and their first meetings sooner or later.
I generally considered "Where No Man Has Gone Before" as being pre-5YM. Granted, part of that was me taking the VHS videos (where I first saw most of the original series) literally in that it was episode 2 and there was no Kirk monologue on the VHS (I learned years later that was actually the opening during at least half the first season, but I didn't know that at the time). And part of it was the set design/uniforms.
My Brother's Keeper also went with that idea. After the events of WNMHGB the
Enterprise was on it's way back to Earth for a refit before they were to start their 5 YM (explaining the changes in set design, uniform and crew replacements).
The Captain's Oath left it a bit more vague, but I was left with the impression WNMHGB was pre-5YM as well (though the events in TCO differed in other ways from MBK).
To me, it makes sense. It's the easiest way to explain in story the changes in the ship, the uniforms and the crew. In MBK Kirk was in command of the Enterprise for several months, maybe just under a year. He was just given command of the
Enterprise so it seems to make sense that they would want to have a bit of a shakedown before sending him off on an extended mission. Originally when I read MBK, which was about a year or two before TCO came out, I just figured the
Enterprise was his first command. I don't disagree with the idea with him having a prior command like in TCO. I just made an assumption. And in retrospect, MBK's is more focused on Kirk's career up the ranks before he becomes Captain and I don't recall anything precluding Kirk having a prior command in MBK, it's simply not addressed. TCO obviously has a prior command for Kirk explicitly, though Kirk's characteristics are similar in both stories (which is why I always said Christopher and Michael Jan Friedman appear to have the same view of Kirk as a straight shooter and not a maverick).
Anyway, I'm getting off track here--however similar both stories are or aren't, after reading both it makes more sense to me that WNMHGB was pre-5ym. Sometimes the simplest explanation is the best to go with, that is, the reason for the differences between WNMHGB and "The Corbomite Maneuver" is simply that the ship had an overhaul before formally starting their 5YM.