Thanks for sharing additional info Nick.
The rules which are missing after update-initramfs, which in my instance are:
- etc/udev/rules.d
- etc/udev/rules.d/41-cio-ignore-root.rules
- etc/udev/rules.d/41-dasd-eckd-0.0.271d.rules

are indeed owned by chzdev:

$ /usr/sbin/chzdev --is-owner /etc/udev/rules.d/41-cio-ignore.rules && echo 
"Owned by chzdev"
Owned by chzdev
$ /usr/sbin/chzdev --is-owner /etc/udev/rules.d/41-dasd-eckd-0.0.271d.rules && 
echo "Owned by chzdev"
Owned by chzdev

Commenting out the part of /usr/share/initramfs-tools/hooks/udev you
highlighted:

if [ $ZDEV_FILTERING -eq 1 ] && /usr/sbin/chzdev --is-owner "$rules"; then
    continue;
  fi

and executing update-initramfs shows that the needed rules are included
in initramfs:

$ lsinitramfs /boot/initrd.img-$(uname -r) | grep udev/rules.d
usr/lib/udev/rules.d
usr/lib/udev/rules.d/41-cio-ignore.rules
usr/lib/udev/rules.d/41-dasd-eckd-0.0.271d.rules
...

and the system reboots correctly.

If my understanding of the system is correct, the problem seems to be
that chzdev is not copying its own rules inside initramfs

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https://bugs.launchpad.net/bugs/2102236

Title:
  plucky/s390x (with root disk on dm?) does not come up after kernel
  update + reboot

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