So, is there a way of changing that? They are identical.
There's an officer trainer in the far west of Qo'Nos that will let you change your officer skills.
Secondly, both have Cannod Rapid Fire, but I don't have the actual skill to use in my tray, what gives?
This game isn't very good at putting powers in your tray automatically. Open the power menu ("P" by default) while in space and drag the powers to your tray.
You can have two Cannon: Rapid Fire skills, though. One will put the other on a short cooldown but you'll be able to use both to keep your cannons rapid firing more often than not. You will actually have both of them in your tray (you will see it listed twice in your power list. Drag both icons to the tray.)