The final round of testing deals only with the handset's compatibility to a network and doesn't require a large number of employees to look at the phone. Why a black box? Most likely to make sure that the carrier doesn't mix up the box with its inventory of Apple iPhone 4 units. You can imagine what would happen if a carrier accidentally sold an iPhone 5 prototype to a customer.
While no one knows for certain that these black boxes contain the new Apple iPhone, what else would be in a special sealed box coming from Apple that can't be opened except by certain people?
source: TheGuardian via RedmondPie