No, I completely agree... Best Buy doesn't have to accept shit if it's as fishy as this, like you said. He VERY well could have swapped it for a fake, retail stores see this kind of crap all the time. He has no proof that he didn't, and it's even more suspicious that he waited so long, and even tried to have it returned at a completely different store, in a different state. The red flag to me is the fact that he's DEMANDING a second iPad for free. It would be different if Best Buy offered a second as reparation for the mishap, but he's demanding one. At most, he deserves a $25 or $50 gift card, and an apology.
I don't know about you, but something of that cost wouldn't go very far out the door without some kind of quick inspection to make sure it's working as it should.