I have no experience purchasing Apple products from AAFES, but being retired Army I have purchased other products from their online store. I have noticed that option showing up on most products that ship direct from the supplier. My most recent purchase was an iRobot vacuum that had the same 90 day option, it was on back order and delivered 30 days after it was ordered.
I think that this is something that AAFES includes to cover the potential longer delays to ship. The best place to get the correct answer is from AAFES. Although when I asked them about my iRobot order, their answer left me somewhat less than satisfied.
