The official software manager on my Fedora system (Discover) presents me with Flatpaks.
If I use Discover for updating ,the Flatpaks will update too.
But when I use the official CLI tool to upgrade the system only RPM packages are updated.
The other package managers on the system are not affected (Flatpaks, Snap, Cargo, PIP).
I think there should be no discrepancy between CLI and GUI interfaces for system updates.
The fact that I should "remember" how to update stuff shows that something is wrong or is not perfect.
There was a time when using the update button of Software Center was exactly equal to running "sup apt dist-upgrade". Everything was simple and straightforward.
What you say is true when this is explicitly stated by the OS.
When the average user uses the Software app they are presented with many Flatpak results. Flatpaks are presented as offerings by the distro, not something "outside of the distro's package manager." Should the average user be supposed to check the origin of every app and know about Flatpaks?
Plus if you use the most popular distro it already comes with default snap apps.
Even on Fedora the average user is presented with many flatpak results when they use the GUI software manager. Not everyone is technically adept enough to check the origin of the app. So it's kind of being forced on users.
Except it doesn't always work. I've seen it stuck and loading updates forever a few times, while a simple flatpak update command did the job with zero issues.
Has the package manager improved? Can it automatically handle dependencies?