The Age of Sail, Age of Discovery, and Colnial Era actually have many different examples of shared power aboard a ship. Take the Golden Age of Piracy as one example. Captains were elected. They had a Sailing Master, who had command of the ship outside combat. Then they had a Captain, who commanded during battle. There were exceptions to that, of course, and they were some of the most famous pirates, being good at two things. In the Dutch Indiamen, a Secretary General would be in charge of things ashore and the Master Pilot would be in charge of things aboard. On a Portugese Indiaman, one guy was in charge of the expedition as a whole while each ship had its captain AND another guy in charge of negotating business deals.
You can even go with a multi-ship Dynasty, if power sharing is an issue. It's not too difficult to draw up a 20-30 SP ship, and you can easily get 2 ships that way, and maybe even a third if you skimp. That might be a fun campaign.
While you are absolutely correct, most of these are variations on the same theme I was talking about. The "Master and Commander" example was meant to reference a style of command breakdown as well as it's specific historical example. The Pirate method is actually how I start any new RT game! The Pc's 'elect' the player that will play the RT. How that player chooses to delegate authority is largely up to them. I also Emphasize that many other organizations on board are their own little fiefdoms! (Especially the Navigator and the Admech priests!).
I once had a situation where one of the Navigators minions refused to take orders from the Ship's XO! She was deferential to the Captain (But still referred him to her Navigator master) but did not see anyone other then the Navigator himself and the Captain in her chain of command. For the Navigator's part, They refused to sanction their underling in any way! They explained (Politely) to the XO that the entire Navis Noblis retinue on board was under contract with the RT's dynasty. This meant they were bound to the Captain and no one else under their contract! Thus, while their minion was a tad inartful , She was not wrong!