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TL;DR: Because Discover uses PackageKit…
Because Plasma Discover and Gnome Software use PackageKit to talk to DNF. PackageKit will download and cache updates for them to be installed later, but if you manually update via DNF, Plasma Discover and Gnome Software won’t know and therefore they will tell you there are still updates when there isn’t and take up space in the process.
Also, Plasma Discover and Gnome Software force a restart after updates because its easier than the user assuming they don’t have to restart when sometimes they should. Just easier to force it…
Those three reasons are why I dislike PackageKit and refuse to use the respective DE software update apps.
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