rbalint, in the output there is some oddity:
"Keeping auto-removable linux-image-extra-4.8.0-54-generic package(s) because 
it would also remove the following packages which should be kept in this step: 
libpam-systemd libsystemd0 libudev1 systemd systemd-sysv udev
(Reading database ... 53554 files and directories currently installed.)
Removing linux-image-extra-4.8.0-54-generic (4.8.0-54.57~16.04.1) ..."

So it says it is keeping linux-image-extra-4.8.0-54-generic and right
thereafter it is removing the same package.

** Summary changed:

- By default settings unattended-upgrade does not automatically remove packages 
that become unused in conjunction with updating by other software
+ By default settings unattended-upgrade does not automatically remove kernel 
packages that become unused in conjunction with updating by other software

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https://bugs.launchpad.net/bugs/1624644

Title:
  By default settings unattended-upgrade does not automatically remove
  kernel packages that become unused in conjunction with updating by
  other software

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