I don't call layering the armor like that a "problem". I call it staying alive while he does his job.
Remember, to rig effectively, he's in VR & probably HotSiming it. That means he has to rely entirely on soaking damage if he's caught in a crossfire. He doesn't know it if someone slips a
grenade into the passenger compartment of his van.
It also means that if the enemy team has a hacker (and if they see drones, they'll hire one quick if they don't have one already and can afford the nuyen), then he probably has Black IC to unleash on the rigger. That's real world damage and distracts him from the job of rigging. If he's hotsiming and jumped in, when the drone takes damage, he soaks damage, too.
So no, I don't see where the problem with him being relatively secure from attacks originating outside the car comes from.
As to whether or not the rigger gets vehicle armor in addition to his own for ramming, full-auto and area effects, it looks like the answer is vague.
The passage is:
If an attack is made against passengers, make a normal Attack Test, but the passengers are always considered to be under Good cover (though the Blind Fire modifier may apply to the attacker as the situation dictates.) Passengers attemptint to defend an attack inside a vehicle suffer a -2 dice pool modifier to their dodge, since tehy are somewhat limited in movement. Additionally, the passengers gain protection from the vehicle's chassis, adding the Armor of the vehicle to any personal armor the characters are wearing. Called shots may be used to circumvent one armor or the other but not both.
In the case of ramming, full-auto and area-effect attacks, both passengers and vehicles resist the damage equally.
Now, reading that, I'm led to believe that you don't add vehicle armor for the three you're interested in. It doesn't spell it out, but the way the section is written implies that vehicle armor is only granted to the passenger if the passenger is specifically targeted.
But, frankly, I think it's nonsense to suggest that being in a vehicle shouldn't help you survive any of those three. The vehicle still catches some of the lead in a full-auto attack and the blast/ram still loses kinetic energy as it travels the frame of the car to you, the passenger. The wording of the section doesn't specifically preclude this option, either, since that last sentence doesn't end "resist the damage normally". Rather, it's a statement that the attack targets both simultaneously, and therefore, both have to resist the damage.
I'd give him the armor, a smart GM is already hard enough on riggers.