That is interesting indeed.

The difference being on other systems the virtual functions are by default disabled which I guess is why no one is running into this problem with other hardware.

An example from a system with the ixgbe driver:
# cat /sys/devices/pci0000\:00/0000\:00\:03.0/0000\:01\:00.1/sriov_totalvfs 
63
# cat /sys/devices/pci0000\:00/0000\:00\:03.0/0000\:01\:00.1/sriov_numvfs 
0
# ls -l /sys/devices/pci0000\:00/0000\:00\:03.0/0000\:01\:00.1/virtfn*
ls: cannot access '/sys/devices/pci0000:00/0000:00:03.0/0000:01:00.1/virtfn*': No such file or directory

While on a system with the Cavium Thunder X card:
 cat /sys/devices/pci0002\:00/0002\:00\:02.0/0002\:01\:00.0/sriov_totalvfs 
128
# cat /sys/devices/pci0002\:00/0002\:00\:02.0/0002\:01\:00.0/sriov_numvfs 
18
# ls -l /sys/devices/pci0002\:00/0002\:00\:02.0/0002\:01\:00.0/virtfn*
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn0 -> ../0002:01:00.1
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn1 -> ../0002:01:00.2
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn10 -> ../0002:01:01.3
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn11 -> ../0002:01:01.4
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn12 -> ../0002:01:01.5
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn13 -> ../0002:01:01.6
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn14 -> ../0002:01:01.7
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn15 -> ../0002:01:02.0
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn16 -> ../0002:01:02.1
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn17 -> ../0002:01:02.2
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn2 -> ../0002:01:00.3
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn3 -> ../0002:01:00.4
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn4 -> ../0002:01:00.5
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn5 -> ../0002:01:00.6
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn6 -> ../0002:01:00.7
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn7 -> ../0002:01:01.0
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn8 -> ../0002:01:01.1
lrwxrwxrwx 1 root root 0 Jun 29 08:24 /sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn9 -> ../0002:01:01.2
# cat /sys/devices/pci0002\:00/0002\:00\:02.0/0002\:01\:00.0/virtfn0/net/enP2p1s0f1/phys_port_id 
cat: '/sys/devices/pci0002:00/0002:00:02.0/0002:01:00.0/virtfn0/net/enP2p1s0f1/phys_port_id': Operation not supported

And this is on by default, without a operator having enabled the virtual functions.

libvirt finds the virtual functions this way:
https://github.com/libvirt/libvirt/blob/0b86e23d25696c08234d4b73c90cef9515befe84/src/util/virpci.c#L2688