Regular Magsafe can start charging at 40-50mm. Power has to go through a lot of packaging layers. If they make an extra-strong in-store charger cradle to boost that distance, it would be possible to reach the phone, and trigger a power-up session without opening the box.
The power detection chip can take very little energy so everything else (other than maybe power-button-press detector) is in super-dormant mode.
On power bootup, the phones can connect to Apple store wifi (preset in wifi defaults), then use key exchange to authorize wifi. Then they can use mDNS/DNS-SD to scan for an update service running on the store network. If found, they can do a key exchange, then download the update, validate, and install.
The whole time, the custom cradle could also be topping up the phones so when the user opens their box, it's charged and they're happy.
Just a guess. Very clever, if true. Also, eminently doable.