I am not certain if there can be a standard solution, the GRbasedIV defaults from the vendor to whom you place the PO. The freight is just a condition in price schema, it is often without vendor, but can have a totally different vendor than the main vendor.
It is probably a design issue which was decided different than expected, whether the GR based IV indicator in the PO is valid for all parties that are involved in the process or only to the main vendor.
I havent seen any docu or consulting/error notes on this.