Weird thought...
What if Buffing just became a core part of the Gunner / Engineer class, and was pushed into a pre-combat role exclusively?
By that I mean remove the Buff Hammer entirely, and allow Gunners and Engineers to hit components repeatedly with the Spanner or Wrench when they're at 100% health to "over-build" them, which triggers the buff. Gunners are the only ones who can buff guns, and Engineers can buff other components (Engines, Armor, Balloons).
It might require the introduction of a new Engineer tool to make tool choice have some deeper choices again, but I think it might make the Gunner effective and distinct while not causing tool slot confusion. It will also help the Gunner have more responsibility on the ship (pre-buffing weapons), and help solidify the buff into a pre-combat tool and not a mid-combat tool. Finally, it has a nice side of effect of discouraging Mallet Gunners, which are a bane to my existence and unfortunately more common among newer players than I'd like.
Thoughts?
EDIT: Might even be worth re-thinking the gun buff in this case. Maybe to make guns more durable instead of giving them more damage? Maybe to give them a bit of both (+5% damage, +25% durability, for example)?