Okay I don't understand it.They deal more damage to armored targets but they lower the damage overall.That means you deal less damage to enemies that don't have armor?Or I am mistaken?
I don't have the figures for enemy armour but lets say a brute has 60 percent damage reduction and your mod has 50 percent negation. Brutes DR is now 30 percent.
The Javelin is unique with regards to this. It doesn't get a penalty when it shoots through walls.It does if you use the piercing mod.
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