The old version and the rework described in the patch noted for U39 states that destro staffs "Penetrating Magic" affects "Spell Resistance" which should only affect abilities that apply magical damage types (e.g. magical damage, fire damage, lightning damage and frost damage). If we compare this passive to dual wields "Twin Blade and Blunt" or two handeds "Heavy Weapon" passives which state "Armor Penetration" we have another penetration type that should affect physical damage types (e.g. physical damage, poison damage, ...).
Since you are already working on hybridization with "Armor" and "offensive Penetration" on Armor, could you either more specifically clarify that "Penetrating Magic" does not count towards physical penetration or change those passives also to match with the new hybridization concept to also grant "offensive Penetration"?
Tank for passion. Tank for love. Tank for life.