We discussed the test with Brian, and ending in inconsistent states can
still occur when running u-u manually/via cron.

In those cases the apt fix does not protect dpkg from being terminated early.
When running u-u manually or via cron it is recommended to use workaround 3. 
from #19, i.e. running u-u like that:
 systemd-inhibit --what=shutdown,handle-hibernate-key --mode=block /usr/lib/

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https://bugs.launchpad.net/bugs/1690980

Title:
  unattended-upgrades does not block shutdown of system, as it is
  designed to

Status in OEM Priority Project:
  Triaged
Status in OEM Priority Project xenial series:
  New
Status in apt package in Ubuntu:
  Fix Committed
Status in unattended-upgrades package in Ubuntu:
  Fix Committed

Bug description:
  Title: No pop-up window to warn users that system should not reboot or
  shutdown while installing security updates

  Summary:
  No pop-up window to warn users that system should not reboot or shutdown 
while installing security updates

  Steps:
  1. trigger unattended-upgrades
  2. reboot or shutdown system while installing packages

  Expected results: There is a pop-up window to warn users that system
  should not reboot or shutdown

  Actual results: There is no pop-up window to warn users

  Additional information:
  $ apt-cache policy unattended-upgrades
  unattended-upgrades:
    Installed: 0.90
    Candidate: 0.90ubuntu0.5
  $ lsb_release -rd
  Description:    Ubuntu 16.04 LTS

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