I just picked up my new phone at an AT&T store. The FedEx discount was applied then and there to the plan. The guy who sold it to me and activated it has a brother who works for FedEx and was pretty knowledgeable about our discount. He was about to try to sell me a case when he caught himself - "Oh, yeah - your discount doesn't apply to Apple products."
So, AT&T products and plans - yes.
Apple products (including the phone itself) - no.
At least according to my local AT&T store.