I too came from an 05 Frontier which got all chipped on the bed sides in front of the rear wheels. Ended up getting bed liner sprayed on the sides which worked well.
As for the wrx, yes, the paint is horrible and the clear is very soft and thin. I live in PA where they dump gravel on the roads all winter. If you want to feel better about your car I'll post a pic of mine at 11,000 miles.
For the chip, I'd just touch it up and get the clear bra.