Taking lines from WNMHGB as irrefutable fact seems a little pointless to me. It was a pilot episode where Spock wore yellow and had "a human ancestor", where Sulu wore blue, and where Kirk had a BFF that never came up again in canon Trek. It's a great episode, but as with most pilots it's not entirely continuous with the series proper.
Before I read about prior Kirk commands in novels and comics, I assumed the Enterprise was Kirk's first command. I guess because of his relative youth compared to the other starship captains we met.