I agree that your admiralty missions and battles with friends, group members or clan members in should be identified different on the open water as right now it's pretty hard to figure out which is the one you want when you're in a heavily populated area.
I don't agree about being able to lock battles though, having battles open in the open world is something which I love about this game and that should be a PVE server only function if implemented at all. I love that I can enter someone's battle and help or on the flip side join another faction's side against a player. Especially if they're of an opposing faction.