NFPA is crazy, you are reading it right. They are really telling us we need to drill more holes. In reality you still have the practical limit of 9 current carrying conductors (using the 90c column) through one hole so it is not that restrictive.
I am still not sure why I don't have to derate until a nipple is 2 feet long, even if it is packed in foam but I have to derate in a 1.5" penetration with some foam in it.