Actually, my rep told me quite the opposite. For normal orders, yes you can specify a different shipping address. But for the iPhone orders, they will be using a completely different system, and you can only have it shipped to the billing address on the account. However, if you have manager access, you can just change the address beforehand, then do your pre-order, and change the address back later. That's what I did... changed it to mine, so I can order, then I'll change it back to my dad's.
Also, since it's a different system, the only payment methods accepted will be credit cards and gift cards. The bill-to-account option will not be available for the pre-orders.