Snap forces updates, and you cannot disable them. So if you use snaps, I guess you can stop worrying and keep going with your usual apt routine.
What about pkcon? I haven't used it in particular, but packagekit based GUIs work pretty well in my experience, and then it supports flatpak/snap/apt/kde addons/etc in one interface, which is better than it was originally.
If you want a single command, consider topgrade. Not sure if it supports Flatpak and Snaps yet, as I do not use those (yet).
Perhaps a small bash script to iterate through all of the package delivery mechanisms' for updating everything?
I use Fedora for work, but ArchLinux at home. If you really want to skip flatpak
then you need the AUR.
I get 99% of my packages via nix and the other 1% through appimages which I can put anywhere I like on my disk
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