This can easily be solved by bundling all update commands into a single command. I have an alias for this, that updates everything with just a command called update. There is no need for an extra software. But you have to figure out the commands and options to do this correctly. For my operating system EndeavourOS, I have this:

alias update='eos-update --yay ;
  flatpak update ; 
  flatpak uninstall --unused ; 
  rustup self update ; 
  rustup update'

then run it with:

update

... which updates the system, the AUR, Flatpak and my Rust environment. You don't need to rely on any third party software to update your system.

Both KDE Discover and Gnome Software offer similar functionality. You should also be able to use them without their respective shells.

Ubuntu's software updater updates both deb packages and snaps. To my knowledge it doesn't do flatpaks, though, as Ubuntu officially doesn't support them.

bauh, it has support for Debian and Arch packages (including AUR), Appimages, Flatpaks, Snaps and web apps.

Cockpit has an update manager built in and has the ability to setup dnf automatic

Different software management systems can interact with Flatpak. I think the KDE package manager can, and the Gnome package manager too, if you install the plugin.

Several distros have those kinds of utilities built in.

Synaptics Package Manager comes preinstalled in lots of Debian derivatives.

Manjaro, Bazzite, and Endeavour have their own bespoke update managers. (Others do, as well, but those are the three non-Debians I've used most recently.)

OpenSUSE has GUI software updates via GNOME package updater or KDE discovery center, but also has GUI Yast software manager independent of DE