I wrote this in another thread, but it is applicable here.
If you've read any business-related books (most specifically "The World is Flat"), you'll be able to understand my reasoning.
No matter where you pre-ordered from, for direct fulfillment to your home/business, they're all going to ship from the same place via the same method. There's a good chance that there are a few FedEx warehouses across the country which have crate upon crate of product that they will begin distributing as launch day gets closer.
Steve's said that apple isn't a search company, and likewise they're not a shipping/logistics company. It would make sense that Apple has never even taken possession of the products following its departure from the foxconn factory, and that in fact FedEx is handling all distribution and delivery logistics.
It would additionally make sense that Apple is able to provide free shipping to all based on a reduced cost per volume of packages shipped via FedEx over the next week/month/year. At this point, it seems just a matter of printing labels on the pre-packaged, one-off iPhone boxes and starting them through the FedEx system. There are likely separate fulfillment channels for distribution to retail stores, in which shrink-wrapped iPhone boxes are packaged "by hand" for distribution to Apple/ATT locations based on reservation volume and BB/RS locations based on a (probably) simple formula taking into account retail and population densities, as well as stock necessary to provide Apple and ATT with sufficient product.
My hypothesis will be generally confirmed if someone who orders two separate iphones receives two phones individually packaged in their own shipping box.