These are all excellent points. I think really it just comes down to the GM showing common sense regarding what will actually do structural damage to the vehicle, as well as what the vehicle can protect it's occupants against and what it can't.
Take a normal car, for example. A car door will not protect you from bullets, but will increase the difficulty to hit you if you're hiding behind it. An armored car would provide actual protection of course, but then you have to consider other effects on handling, acceleration, and top speed. Furthermore, the bullet is unlikely to do serious damage to the car unless it hits in specific places (hoses, wire, radiator, gas tank). Of course, it depends on the gun as well. There are guns, such as the Marine Corps .50 cal sniper rifle, that can supposedly puncture an engine block. Certainly with an AP round, anyway. Normal grenades are certainly capable of damaging a car.
These examples make me skeptical of creating or using a separate scale for vehicle damage. Besides, I always though Paladium's megadamage system was a horrible kludge.
