No, programs not downloaded with the package manager are also not updated by it. Many Programs, like Firefox and probably Mullvad bring an autoupdate feature that is enabled if they are installed manually. If an update is available you will probably get a notification in the app to restart your browser so that the changes are applied.

Last time I looked it had way less features then yunohost and its closed source.

Des, it has, what most others lack: Single Sign In and many Apps.

Last time I researched it I didn’t found easy answers. Do you have an easy script?

They just asked 1502 people by phone.