IMO the proper fix involves several changes which I collected in this GitHub 
branch to be merged
to upstream:
https://github.com/rbalint/unattended-upgrades/commits/lock-handling

Since the changes are extensive I would prefer merging them upstream,
releasing them to sid, then Artful, and then they can be backported to
Xenial and other releases. It looks like to me that more code needs to
be backported than half of the delta between releases thus I propose
SRU-s practically syncing latest unattended-updates to supported
releases.

Testing of the new code is appreciated, but please let u-u be triggered
by the apt-daily* timers because sudo does not protect u-u from being
killed as Ethan pointed out in #25.

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

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

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