I would be pissed if I had a car that new with this issue. Especially since it happened to mustangs years ago and they should know how to prevent it from happening.
Having said that, I think you should be happy they are planning on replacing the whole hood. The dealer my sister went to said they would just repaint her current hood. She pointed out that there have been lawsuits about this because the hoods just get bubbles again. Something to do with the minerals in the hood material. So She is having to fight with her dealership to replace the hood at all.
Hopefully the new hood they send you doesn't have the same problem.