boarding a flagship

[goofy007]

At this time you can not get a larger ship without unlimited access.

If you can defeat all the enemy crew members in combat, the ship is yours! Claim her cargo or other Quest–related items.

I believe they are just using colorful language when they say the ship is yours. You receive better and more cargo from sinking a flag ship and you can receive other quest items at the same time but the ship will always sink.

You can not commandeer a flag ship and make it your own. I have boarded may flag ships at many levels and they have all sunk. Once the crew is removed you will be taken back to your own ship.