From what I have heard from Apple Store Employees who I asked about this topic, at the moment they are doing nothing. Technically someone could grab something from the shelve, look like they are checking out on the phone and walk out and there is no verification that someone has actually paid for the item.

It is going to be interesting how, or even better if, they are going to tackle the issue of loss prevention or if they are going to consider it an operating loss.

The interesting thing is that even before they implemented the self-checkout system it was based on the honor system as well. Nobody has ever asked me if I had paid for the items as I was leaving the Apple store. Nobody flagged me down as I was holding items to pay for them. I didn't have a physical receipt, just one they emailed to me and I've almost never asked for a bag so they can't identify people who have paid vs those who hadn't paid that way...