On the issue of who's in command ...
I note that near the end of "Journey to Babel," Kirk is badly wounded but remains on the bridge as long as he can during the climactic crisis.
Once things calm down, Kirk says "Mister Chekov ... take over" as he slowly departs.
Spock is in sickbay, donating blood too his father. Scotty is busy below, keeping the ship together. Sulu is absent (I think he was hangin' out with John Wayne on a film set).
Lt. Uhura is clearly in the long shot as the captain exits. In fact, she's within three or four steps of the captain's chair. Yet, Kirk designates Chekov, who recently came aboard and who hasn't any stripes. I know that Kirk is wobbly, but it's still curious.
(I had prepared a screen grab, but for some reason I can't get it to display.)
https://imgur.com/a/KgeJztC