Here something that I don't think you have thought about yet. What if the dealership re-cleared the trunk before you took delivery. Have you had a bodyshop take a look at it. It might be that if there were some scratches and they were only going to re-clear the trunk they may have left the letters on when they did it. If that is the case the missing clear isn't missing clear it is new paint that wasn't applied under the existing letters. Just because it was a brand new car does not mean it did not get scratched in shipping and needed to be touched up. Most Dealerships will not admit that this is the case but a good body shop should be able to see if this is the case.
Just a thought