Well he doesn't, unless he's using a bond mystery.
Chances are the quest doesn't pick up on wither he "has" a bond mystery or not & just uses the base mystery in it's parameters for quest completion, seeing as we don't get many fixes for similar things you might as well just pick a ninja that paralyses.
Correct
It's based on their regular skillset.
Bonds is a feature that provides them an additional mystery.
Arena and other mission will always use base attributes