They don't just "put a Magic Trackpad in an iMac box." If it's custom config, they don't have it boxed.
There are, basically, two fulfillment processes. In one, they have boxed, standard-config iMacs ready to ship. You order one, your name gets printed on a label, they slap it on one of them, and it goes onto the boat from China with all the others.
In the other, they have unboxed iMacs. You order one, and it goes from station to station along the shipping line as people check the order, put in the correct whatsit, and send it on to the next station for the next whatsit. At the end, they check it again and box it up, then they slap the label on it and it goes onto the boat.
Think of tailored vs. off the rack clothes. Even if you don't need any big alterations, it still takes way more time.