I don't have an explanation of the behavior of pam-auth-update, but
Debian bug #923362 has also just been filed regarding pam_systemd
inexplicably getting disabled, and may be related.

** Bug watch added: Debian Bug tracker #923362
   https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=923362

** Also affects: pam (Debian) via
   https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=923362
   Importance: Unknown
       Status: Unknown

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https://bugs.launchpad.net/bugs/1817897

Title:
  attempting to enable fingerprint with pam-auth-update breaks gdm

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