> I don't understand the distinction you use here.

Distinction: https://news.ycombinator.com/item?id=49683258

I use "dnf" to upgrade my system and "flatpak update" and "brew upgrade" to upgrade the apps I've installed.

An app like VirtualBox does not install using Flatpak or Homebrew, so I would use dnf for that. It's usually an app or two that doesn't work via Flatpak/Homebrew/AppImage that I need to install using dnf.