Neither the FAR nor the DFARS specifically addresses the issue of shipping charges and the requirement to obtain a sepatate bill of lading from the vendor.

However, the FAR does express in FAR 13.301(b): (b) Agencies using the Governmentwide commercial purchase card shall establish procedures for use and control of the card that comply with the Treasury Financial Manual for Guidance of Departments and Agencies (TFM 4-4500) and that are consistent with the terms and conditions of the current GSA credit card contract.

In this case, you would need to check with your agency to see what type of procedures they have developed.