OK, I got a lot further with this. It was, surprisingly ;-))), PEBKAC.
Started sys-net with HVM and the kernel as "none" worked in the sense that the VM boots and no PCI errors are thrown around.
What doesn't work at the moment, is that no connections seems to be possible through qrexec in HVM mode and so since there is no GUI connection possible and so the VM shuts down.
In PVH mode, everything works very smoothly and without issues for VM's without needing pci passthrough.
Will have a closer look...
Best,
Jurre