I don't remember what I did in the past, but I was able to reproduce the dialog 
with the following steps:
1. Upgrade fully and reboot the system.
2. Downgraded a package:
sudo apt install unattended-upgrades=1.1ubuntu1
3. Disabled u-u:
sudo dpkg-reconfigure unattended-upgrades
4. Opened Gnome Software (Ubuntu Software)
5. Clicked on Updates tab, then on the refresh/reload icon in the upper left 
corner.
   Gnome Software printed "Looking for updates", then misleadingly that 
"Software is up to date" despite u-u is still not upgraded.
6. The prepared-update file is now present:
$ ls -alh /var/lib/PackageKit/prepared-update 
-rw-r--r-- 1 root root 93 srp  18 12:24 /var/lib/PackageKit/prepared-update
7. Clicking on Shutdown now offers installing updates which is executed, too. 
Upon next login a report is shown about installed updates.

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https://bugs.launchpad.net/bugs/1775226

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

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