As a professional production guy, here's my take on it.
If it were a non-apple feature film/production, they wouldn't use Apple employees as lockdowns/PAs to keep people away from the store. They would be renting cops and paying PA's $75 for the night.
If it were an iPhone 3G commercial, they wouldn't have the store's regular employees anywhere nearby. As we all know, Apple guards their secrets very closely, and wouldn't allow any employees anywhere near the glass store. We also know that Apple's advertising partners have signed a lot of NDA's, and wouldn't tell anybody anything over the phone... especially the concept of the ad itself (the Big Lebowski bollocks). We also know that apple ads are shot on soundstages, with small crews. This is not the case here, as it is in a store, and employing a relatively large production crew.
My bet is that it's some sort of sizzle reel/presentation video for the upcoming keynote, or possibly a future keynote. They also may be shooting an internal video, but they have the mockup store for that. They also wouldn't need a Jib. A possible explanation for that is having the store closed for a separate (internal/presentation) video, and rolling out a Jib for stock shots as long as they have the lighting and film permits.
Bottom line: Too many people/wrong location for an iPhone ad. They also wouldn't need exterior shots of an Apple store for a national iPhone spot. It's something else.