That was the same as me. I asked them not to drill the plates but stick them on. They actually had the plates in the car with double sided tape so I could put them on and know they hadn't been drilled underneath!
My last car before the Golf, I told them again from the onset not to drill my plates. I also reminded them with every email and was assured this wouldn't happen. So when my car arrived and had been PDI'd the dealer (100 miles away) sent me pictures of it and yes you've guessed it, they had been drilled on. They had to get it smart repaired before I even picked it up!!!

The plate holder is actually gloss black so you won't need to take that off as I think with the contour of the bumper a plate wouldn't sit right without it.