Is it possible to add-on a small rework of rank structure with lowest officer rank Lieutenant, Lieutenant commander, Captain, Rear Admiral and/Vice Admiral, with admiral level able to be held in fleet or promoted to fleets of their own to protect colonies. Your character would be in essence Ruler and Admiral of the fleet, which they pretty much already are in truth.
Possible larger rework~These officers could also have a chance to die or be captured in battle with chances of capture held against their current ranks and/ size of their fleet for admiral lvl officers. Payment could also be reflected from their ranks and possibly faction diplomatic level at the time of parley. Maybe the faction holding the prisoner calls you after a period of time to arrange for transfer? Would flesh out the use of a military high command and add more flavor.
And I'm totally on board with the OPs idea sounds like a great idea.