That's true for the store (Pop Shop), but not for the CLIs (apt and flatpak). If an app has only a .deb or flatpak version, it's not clear which will be install

That's true for the store (Pop Shop), but not for the CLIs (apt and flatpak). If an app has only a .deb or flatpak version, it's not clear which will be installed. If there are multiple versions, you get a dropdown menu to select one. Unfortunately, some apps are listed more than once (different packagers, I assume). Ubuntu, on the other hand, will sneakily install snaps via apt.