One of the points on that link is: "Offers detailed tracking visibility for every package in the shipment".
When they load the shipment in China, each container has a bar code. They scan each box as it goes into the container so they know what's in there. The containers go into a plane that also has a code. When that plane lands in customs, they can apply an updated "scan" to each package on the plane with one "swipe" Each package in the shipment does get updated scans at each step of the journey.
Exactly, this is how FedEx does bulk shipments as well.
There is also provisions for fast customs processing as well that UPS and FedEx uses. It allows pallets that are identical items to be accounted for in the manifest and in customs paperwork and pass thru with little more than a sniff of a K9.