I have about 600 hours in SOT so I can answer this.
So honestly that’s a TON of progression without risk, but it’ll be slow going. Emissaries allow you to increase your rewards for a particular faction (reapers, hoarders, merchants, order of souls) so you can’t get those bonuses.
You need to be a pirate legend to captian a ship, and you need three of the primary factions at level 50 to become a pirate legend. Literally no difference beyond achievements and cosmetics. Captaincy just let’s you “own” the ship that spawns in, and essentially designates a player as “leader” whereas in normal play its ad hoc on who does what. And a captained ship just has a name and extra cosmetics anyway.
Can’t earn rep for reapers which kinda sucks, but makes sense. It’s the pvp faction. But many players do pve reapers as well.