Are you wanting to remove the skin for all of the buttons or just the 3rd bar?
Just quickly skimming through nMainbar...
It looks like you could just comment out SkinButton(self) in the ActionButton_Update hook and it wouldn't skin any of the standard buttons.
The other choice I would say to try is in the SkinButton function, after the declaration of buttonName add
Code:
if buttonName:find("MultiBarBottomRight") then return end
Not sure what the name of the 3rd bar buttons are in the addon so you'd have to alter that yourself.