Armor vs. Protection - question of piercing and negation

[PvK]

Seems like:

(Wpn+Str+2D6) - (Protection + 2D6)/2

where the /2 is the armor penetration, would not make sense, because for targets with zero protection, the damage would be:

(Wpn+Str+2D6) - (2D6)/2

meaning that armor penetration would do more damage against targets with no armor, making the base damage stat mean different things, even when no armor is involved.

PvK