Hello,
it sounds unusual to me the fact that the packaging material is displayed as a line item in the delivery. Usually you go to the "Pack" screen, there you select the items of the delivery, assign the packaging material and carry out the packing. The packaging material became part of the Handling Unit.
Is the line item of the pallet idetified by a different item category?
If you don't find an alternative standard solution, you can clear the weight of the pallet line item from the include MV50AFZ1 in userexit_save_document_prepare.
Best regards,
Andrea