Finally closed my ticket with Mazda corporate today. After going back and forth with my local service department, they basically told me to there was nothing they could do. I was told that the chips in my hood were normal rock chips, and that other people's experiences that I have seen on this forum (and others) doesn't prove that this issue is a problem or flaw in any way. When I asked about the paint pen being on backorder since early summer, the rep at Mazda corporate told me that the paint quality issues they're having with that have no correlation to the paint issues owners are having. Riiiight.
Got my car in April, and had a cluster of chips on the hood within 3 months. Since then, I've had more chips scattered throughout the hood and quarter panels. I spent a good amount of money getting my windows tinted soon after I purchased the car, and would have been happy to get some 3M as well, had I thought I needed it.
Might just try a touch-up kit I've seen here, but am really disheartened.