Just on the face of it an exceptional flintlock SHOULD be better in combat in some way. If my match grade rifle can't shoot as well as an off the shelf model I would be not happy with the gunsmith or company that sold it to me. Any exceptional item should grant some benefit or nobody would go to the trouble of making them in the first place. Just common sense. And I prefer a degree of common sense and civility at my game tables.
Now from my experience a better grade firearm is generally made to be more accurate so I would say an exceptional firearm should get a +1 to hit. At least that makes sense to me. I look forward to hear what the powers that be have to say. Take care all.