depends on how it is used, I mean, matter manipulation applied to combat can... transform someone into water, air (simple applications, that is) so if the user isnt resistant to this (like in sains seiya, where everyone is), yes, it is a negating conventional durability. Reality warping and Space-time manipulation serve as well.
About whis and vados: they have never shown to do such a thing in combat, so it shouldnt be assumed they can use it this way (iirc whis rearranged goku's and vegeta's clothes, vados created the arena in the neutral planet...).
If anything, I vote for Giratina, for reasons already stated.
