I generally install apps (graphical programs I guess) using flatpak, and then anything non-graphical or system-related programs using the native package manager. The main exception is apps that already have a sandbox like Firefox or Chromium, which I install using the native package manager to avoid weakening their native sandbox.

My main gripe with flatpaks is the sandboxing kind of sucks, but it’s still better than nothing. The other issue is apps will sometimes take a long time to move off EOL dependencies.