As some of the Dust guys created AT43 i dont recall the pilots having any affect on their bots in that game so I can only guess that is the same intention in Dust other than the special skills if applicable.
As promised the response from Fantasy Flight.
You recently asked some questions about Dust Tactics:
My question is about the pilots skill some of the new Russian heroes have. When the hero is piloting the walker, do they count as one unit? In the case of a hero joining a squad. The two pool hit points and you may choose who takes damage, hero or squad members. Is this also true when the hero is piloting the walker?
Answer:When a hero is piloting a walker, or any other vehicle, they activate at the same time, but they do not count as being a single unit, such as when a hero joins a squad. The vehicle and its pilot DO NOT pool hit points. While piloting a vehicle, all damage is applied to the vehicle being piloted until it has been destroyed.
I hope this has answered your questions. Happy Gaming!
Assoc. Miniatures Games Producer
Fantasy Flight Games