I wondered about this all the way through Borderlands and now I'm seeing the same thing in Borderlands 2. If a weapon has, for instance, 200 damage, and a modifier that says "+20% weapon damage", does that mean that the weapon actually has 240 damage or that the weapon had 166 damage before the mod was applied?
The answer to this question sort of answers the question for Borderlands, but I'm still not sure in Borderlands 2.