Try to use rd.qubes.hide_pci grub option for your 10000:xx:xx.x devices like this:
UPD:
On second thought maybe you won’t be able to hide them with rd.qubes.hide_pci since Qubes OS is handling this and it won’t see these 10000:xx:xx.x devices as it can’t see them in qvm-pci.
Maybe there’s some Xen option for this as well but I don’t know of it.