having worked for a distibution centre (not apple) there are 2 main process for a product launch which is usually:
you'd have a seperate floor area for each different product.
seperate teams are then given their sheets of orders
hundreds of temporary east european workers grab the product, put them in the cardboard boxes, slides them down a conveyor to be filled with air bubble packing material, sealed and transit label attached.
they they get palletised for the courier, who normally leave a few trailers out back so it's loaded and ready to go when the driver shows up.
courier will then take it to the airport or a main courier distribution hub (depending on location)
i assume at some point in there, your gift message is added.
For mixed orders/alternative way: a conveyor belt with your cardboard box with your order sheet in it and gift message go around, and workers place your phone into the box and send it on it's way down a specific conveyor belt for either a different product to be added to the box or down to be sealed and labelled.
the orders are usually sorted by product (and i have no idea on order of the orders) - so one team will have all single orders of 16gb white, another will have 32gb black etc... so you don't have a mass of workers scrambling around grabbing the product
Pure guess: there are about 3500 iphone boxes (not customer orders) per pallet based on size of iphone box and how many you could fit onto a full sized pallet and how many layers you can stack them.
it doesn't explain why most of the black 4S orders have been fufilled more than white, but that's my 2pence on logistics.
You can take it with a grain of salt if you wish - product launches will change warehouse configurations depending what is being launched so all above could be crap.