Software Updater /update-manager i has a built-in function called phased updates.
Ubuntu software's update system does not.
This, of course also leads to a small annoyance, as the Ubuntu Software program has a notification setting that Ubuntu has decided to have launch at start-up.
So when you run the software updater, randomly if any updates are available, the notify-bubble in the top right corner of the screen will tell you, even if the software updater you just ran shows no updates.
A quick tip for this, if you prefer to just use the software updater for updates, is to open the program Startup Applications and uncheck the gnome software entry.
That'll stop those particular notifications.
For what it's worth
Ubuntu software vs Software updater different updates
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