After a discussion with Michael Vogt I tested this with unattended-
upgrades version 0.92ubuntu1.4 from yakkety-updates and observed the
shutdown blocked temporarily (message in plymouth about updates being
installed) when I shutdown the system with unattended-upgrades running.

I was connected via ssh when running the unattended-upgrades and saw the
following:

Preparing to unpack 
.../18-libreoffice-style-galaxy_1%3a5.2.2-0ubuntu2.1_all.deb ...
Unpacking libreoffice-style-galaxy (1:5.2.2-0ubuntu2.1) over (1:5.2.2-0ubuntu2) 
...
Connection to clean-yakkety-amd64 closed by remote host.
Connection to clean-yakkety-amd64 closed.

In plymouth I also saw the message about "libreoffice-style-galaxy".
Could you please retest and ensure you shutdown the system when packages
are being unpacked / installed?

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

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

Status in OEM Priority Project:
  Confirmed
Status in OEM Priority Project xenial series:
  New
Status in unattended-upgrades package in Ubuntu:
  Incomplete

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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