Interesting when playing with my friends we always have at least one gunner, sometimes two.
My understanding of the problem is quite different though, to me each class as an item slot in each area of expertise, and two additional in its own field.
The problem comes to that:
-To control the boat, just click on the helm.
-To use a gun, just click on the gun.
-To repair a piece of equipment, just click on.... *OUCH* no, you can't.
so the simple fix is to allow repair/rebuild by simply clicking on the piece of equipment. In that case your item slot in each field is only ever a bonus, not a requirement as it is for the engineering slot item currently...
(Just to be clear, that would be a slow repair/rebuild, maybe equal to the current in game worst repair and rebuild values.)