Yes. virsh define (but not start) so that libvirt will create the
randomized MAC, then use libguestfs-tools to modify files residing in
the guest image, and then finally boot the guest.
Better yet, is there a way to simply control the assigning of the eths in the generic xml file used to create the VM?
Libvirt passes the devices to the qemu command line in the same order
that they appear in the XML. It is not libvirt's fault if qemu then
takes the command line arguments and presents it to the guest in such a
way that the guest can initialize the devices in the order in which a
bus scan finds them, rather than in the order they were presented on the
command line.