@Brian Murray
It seems to me that Yakkety (16.10) deals better with a reboot while 
unattended-upgrades is running.

After I shutdowned system by GUI, I saw the following message.
"Unattended-upgrade in progress during shutdown, sleeping for 5s
Progress: 67.5656 % ......"
(Please check logs as attached)

And, I still can login to Ubuntu desktop after shutdown.

** Attachment added: "logs of unattended-upgrades, syslog, dpkg, and apt"
   
https://bugs.launchpad.net/oem-priority/+bug/1690980/+attachment/4883195/+files/log_0525_16.10.tar.gz

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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:
  In Progress
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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