Q. If my Active Pokemon has an owner in its name, and its attack does damage to my own benched Pokemon, would Ledian's "Powder Protection" protect it from such damage.
A. Yes, that is correct. (Nov 18, 2004 PUI Rules Team)
Same concept applies.
According to this, if you choose a Pokemon that is protected, then the damage is weaker/unharmed.
Order of attack:
Choose to do something > Ability > The effect with ability affecting it > final result.
Therefore, the damage is chosen,
ability is noted,
benched are completely protected from attack,
Hm, not sure what else to say.