two things really why; tradition - Commander Jameson of original Elite. also a captain is usually in charge of a multiple crew ship like a capital ship, or a liner. yes i know we can buy those and multicrew is a thing, but its still not really a bunch of npcs you are just driving a bunch of other commanders around in a drive by shooting situation. not the same thing as being responsible for a lot of npc crewers.
the rank is more naval than it is army. so the thing about unit commander and captain being under them is not relevant - since in the navy i knew, a commander or lieutenant-commander might command a small vessel but a destroyer or frigate or aircraft carrier would have a captain in command. this brings up the question of the federal corvette - but in the second world war corvettes were commanded by lieutenants and commanders, rarely by captains in the royal navy. now if the corvette was a true capital ship then you would have to be a captain. and probably in the regular federal navy lol.