Somewhere in the mods section I've heard people mention an improved qualification mod that improves them, I'd look around there to start with. Not sure how/what it does, its on my list of things to look for today, I too have wondered about such things - like the helmsman qualification. Way things stand any officer can navigate the boat (something that wasn't true, besides the captain most officers wouldn't know how to navigate unless they were learning for themselves so they could get their own boat) and having the qualification doesn't seem to have any positive effects.
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