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The holes are used to properly align the emblem - I imagine the manufacturing process improved so they didn't have to worry about emblem alignment issues.
The simple answer for eliminating them is time and money. The holes probably took an extra step punching them out of the sheet metal. The little extra plastic on the emblem prongs might cost an extra cent to make in material. It’s certainly to save money in some form or fashion.
Your PPF guy should remove the emblems to apply the wrap. If there are holes have him reinstall the emblems if no holes have him leave them off. Seems pretty simple...
I think some of the early VINs had holes, but they changed that very early on. I'm pretty sure even mine #36xx doesn't have them - which is why my back one was pretty crooked and had to be replaced.
For ease of detailing.... I have snagged these puppies and the DUAL MOTOR letters would have to be replaced if I were keeping them because they are out of alignment. If I add stuff back it'll be my choice.