Heatsink clip overlaps with engineer tools, Impact bumpers overlap with engineer, and ramming/moonshine overlaps with gunner.
Overlap is ok, it just allows everyone to work together for any goal. When all the ship has to do is get somewhere quickly, why should the pilot be the only one doing anything special for it? When getting flamed to hell, why should gunner have no recourse? When your ally is tearing up the blender that has you locked down, why should the pilot not be able to help you stay alive(drogue chute)?
Every class has it's specialty, but having the whole crew engaged is hardly a bad thing.
That being said, buff hammer is the main reason we don't see gunners. We can bring gunner up to the level of engineers instead of bringing engineer down. For that matter I'd like to see pilot tools being a bit more varied and powerful as well, 4 engi ships are not uncommon.