I can't answer that, but logically if most VW Group cars have these square pads and adjustable pillar like stops, then why shouldn't your one, someone maybe needs to post a picture from the underside of a bonnet of a MK3 pre-face lift Leon to help you here. The other thing being, why would there be a couple of unused holes on that bonnet if the later bonnets also had these holes but they were filled with buffers? A picture from a pre-face lift Leon MK3 would sort this out.
Edit:- I think that the square pads butt up against the lock carrier and the buffers butt up against the metal brackets near the lock carrier.
Edit:- I think that the square pads butt up against the lock carrier and the buffers butt up against the metal brackets near the lock carrier.