Piercing is a tricky thing. It's not a simple graph of penetration ability to penetration score. (Even if this was a simulation, which it is not.) What needs to be taken into consideration is the target's kill value as well. The bazooka rolls a much higher die than the GL, so is more likely to reach the kill value of a basic soldier and remove the save altogether. On the other hand it has less penetration than some tank guns, who only have a penetration of 1. This lets the bazooka effectively deal with infantry without overpowering tanks.
My favorite example is the schürtzen on the PzIV, which gives it a re-roll on its side armor. At first I thought this was silly, as it is only meant to stop infantry based AT weapons. Then I took a closer look and noticed that the armor save on the PzIV's sides is rather poor, so any tank gun's penetration would ignore the side armor altogether, leaving the side armor (and re-roll) for use against weapons with low penetration, those mostly being bazookas, at-rifles and the like. See how that works out?