OK, first the relevant parts of the rules:
Small-arms firing on a hex that contains both vehicle and non-vehicle units must either target a specific vehicle or all non-vehicular targets in the hex.
Passengers are considered part of the vehicle in/on which they are riding.
If the attacker’s modified die-roll is greater than the defender’s modified die-roll, the target vehicle and all passengers must take a Damage Check (DC); the vehicle goes first. If the vehicle is buttoned, only external (PO or PPO) passengers take the DC.
If there are multiple units in the target hex, randomly determine which target the Sniper attacks. The Sniper’s attack only affects one unit.
So yes, passengers are considered part of the vehicle but this is only for the target type (vehicular or leg) determination (and stacking limitation too). It does not means they are the same unit, it means they are the same target. Then, the rules specific to the snipers kick in; the sniper can only affect one the units targeted so either the vehicle (crew) or the passengers.
Imagine your sniper directed his fire at a hex containing a unbuttonned vehicle with passengers inside, accompanied by one squad and a leader on foot. If he chose the leg target, you would then roll to see if its fire affect the leader or the squad right? Well, if he chose the vehicular target, you would decide if it affect the vehicle or the passengers inside.
At least, that is how I see it now. I could be persuaded that only the vehicle can be affected in the case of an unbuttonned armored vehicle but my reasonning above would still stand in the case of an unarmored/open top vehicle.
