I can confirm that clicking the refresh button in the title bar in
gnome-software's update tab triggers packagekit to write
/var/lib/PackageKit/prepared-update, which in turn makes the shutdown
dialog offer to install updates before shutting down.

A few observations:

 - contrary to what's stated in comment #2, I observe that ticking the
checkbox results in updates being actually installed at shutdown
(although I don't know what happens with updates that require user
interaction)

 - gnome-software's updates tab says the software is up-to-date, but
there are actually 5 package updates available, and they are listed in
/var/lib/PackageKit/prepared-update

 - during my tests in a bionic VM, I also observed once that prepared-
update file being created without interaction with gnome-software: I
simply ran "sudo apt update" in a terminal window, then requested
shutdown, and the dialog offered to install updates, so something else
also triggered packagekit

** Changed in: gnome-software (Ubuntu)
       Status: New => Confirmed

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You received this bug notification because you are a member of Desktop
Packages, which is subscribed to gnome-software in Ubuntu.
https://bugs.launchpad.net/bugs/1775226

Title:
  Gnome Software offers installation of updates on shutdown
  independently from update-manager and unattended-upgrades

Status in gnome-software package in Ubuntu:
  Confirmed

Bug description:
  In Ubuntu the GUI for upgrading packages is update-manager allowing
  debconf questions to be answered when needed and Ubuntu also offers
  unattended-upgrades for upgrading packages in the background and it
  keeps back packages from upgrading when configuration-file changes
  would need user interaction during the upgrade. Unattended-upgrades
  can be configured to perform upgrades during system shutdown.

  Gnome Software in Bionic started offering performing upgrades during
  shutdown using PackageKit independently from update-manager and
  unattended-upgrades without offering all of the features of either
  one.

  Unless there is a decision to fully switch to Gnome Software I suggest
  disabling the "Install pending software updates" on the shutdown
  screen to avoid confusing users.

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https://bugs.launchpad.net/ubuntu/+source/gnome-software/+bug/1775226/+subscriptions

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