I prefer jockey seats for the simple reason that its easier to stand up quickly "if the going gets tough".
I totally agree with the need to be on your feet in choppy conditions.
I'm a noob, but this is not intuitive to me. I stand when puttering around the harbor, or at speed when it's flat. When it's rough, I sit on the jockey. I feel there's less chance I get thrown while on the jockey seat. Standing perhaps lets your legs absorb the blows instead of your back. Is there a correct answer, or just personal preference?
I find the jockey style quite comfortable, but I've never been out for more than 2-3 hours.