He's a social scientist and as such would have been wearing a blue uniform pre-command.
Picard was an archaeologist, a thespian and an endurance runner, equestrian and occasional fencer by onscreen description. The only indication that he had command training came from the fact that he wore a red uniform and commanded starships. Chakotay should be no different a case... Seeing him in starship command should not be a dramatic surprise, as his introductory shot in "Caretaker" had him in starship command, and the renaissance man background then follows by precedent.
unless they REALLY had it in the back of their head he was forth in command of Voyager
There's a good reason for Janeway to emphasize such a thing: Tom is basically the most senior of the non-Maquis aboard, after the CO herself and Tuvok. Perhaps not the most trustworthy of the lot, but the most senior nevertheless. And he owes his rank, position and indeed personal freedom to Janeway in a very special way.
Except that there are
other Starfleet senior lieutenants there, and Tom gets bumped down to junior after the first season. But not that many, and not in red.