Apple has at last one mock store in Cupertino that they use for training and internal video. Considering that usage of that is free, and it represents more peoples' local Apple stores, that's what they would use for the store tours. Taking into account the amount of time that they have for setup, production, and wrap at the cube (12 hours), there is no way they would get something like the virtual tours banged out. Setup with jib, lights and limited access (the single entrance) would take at least 2-4 hours, and wrap would be 1-2 hours, leaving them around 8 hours to shoot whatever they're shooting. They would not put that kind of time constraint on something as important, and long as the guided tours.
It's interesting to note that there's been no reports of actors or extras being on location. We know that there is talent somewhere (PA with blue shirts), but the fact that they're not making the store look filled is interesting. If it were, for example, an iPhone ad showing it's ability to video chat across the country (again: example), they would want to make the locations look natural and real. Instead, they're simply focusing on the store itself.