Welcome aboard, K'iirk!
I like the idea of Command (Department). I like it so much, in fact, that I've been using it in campaigns for some time.
In my games, part of department head training includes either Command (Starship) or Command (Department), depending on the department and character type.
For instance, in my previous game, I played a Chief Engineer. He was good at commanding in Engineering, and commanding people like him (Engineers), but he wasn't so good on the bridge (in Holo-sims, at least). His command skill was Command 1 (Engineering Personnel) 4, and I thought that reflected his command areas well enough.
Something else that I use is Administration (Department). Just because you can handle Engineering, for instance, well, doesn't mean that you can handle the entire ship, right? 
In the end, I created a variety of specializations to further "flesh out" the skills that a department head should have. It makes for better characters, I think, as well as more specialized characters, and it made Branch Officer training a lot more interesting, as well.
Greg
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