It seems the PCI-e root ports on the KGPE-D16 have ARI which is needed for SR-IOV, however it is not reported via # lspci -vv I assume that is why the VF's are not assigned to IOMMU groups and thus can't be assigned.
I am running coreboot v4.5 (I forgot to note this as it is another late night)
Tim was the ARI feature implemented when you guys did the programming? https://support.amd.com/TechDocs/44549.pdf