If Apple want to slap your device down on a pad and have it update the OS and set up a phone from an iCloud back up then they will need to find out a way of doing it real quick. Sorry but I am not waiting about for an update to complete or for the phone to set up.
Now, if they added an extra 30-60 minutes to in store pick ups (and confirmed your credentials/back up) then sure I wouldnt mind turning up a half hour/hour later but I'm not going to a store and waiting.
How would that work for people who walked in and wanted to buy a phone there and then?
It's not too difficult that Apple could set up their stock rooms with X amount of updating pads. I don't know... say they had 200 iPhones in stock but they had 50 iPhones on the pads at any time. They could only sell the iPhones that had completed updating on the pads. Each time a phone is sold they add a new one and that goes to the end of the queue for sale.
Backing up in store isn't something that can be done "behind the scenes". If you want your iPhone restored to a back up then you can book that time to get it done or do it on your own time.