I had the same thought, although it's possible it only takes a few seconds on the pad to start the process. There's no way it has to sit there for the whole update. It's quite possible that they have to check in each box individually anyway, so this might not add that much time. And it could outweigh the time cost of helping customers with updates post-purchase (or allow them to manufacture/package devices further in advance of the release candidate being available, which could be even more valuable).
Regarding the in-store experience, I have had similar challenges. I walked in wanting to buy an iPad, and knowing exactly which model I wanted (and that it was in-stock at that store). The employee asked me "if I had an appointment". Since when does one need an appointment to purchase something off the shelf? Crazy.