Out of curiosity, I've just had a look at the same location but on the other side of the bonnet. There's a tiny mark there too. Again too small to have noticed without really looking for it. So I think these are from the clamping system used when the under frame is attached. The paint prep folks (if there are any) probably felt they'd cleaned them up perfectly and they very nearly did.
Car is on its way to the scrappy as we speak!
I have not been able to spot anything on the other side, however the issue on the drivers side of mine is more pronounced than that shown in your pictures.