Today we implemented two additional customer reference fields which can be set in the shipment editor.
Fields #2 and #3 are not always transmitted to the courier and are not always present on the waybill but they are recorded in our database for presentation on customer invoices. These fields are also present (and have been for imported shipment records) on the CSV invoice file.
Currently all three fields are present on the FedEx labels and we will continue to implement them for other carriers.