Flatpak doesn't prevent anything, but it does provide a way for users to avoid those bad things. The format is likely to give Linux users a slightly more BSD-i

Flatpak doesn't prevent anything, but it does provide a way for users to avoid those bad things. The format is likely to give Linux users a slightly more BSD-ish separation between core system software and third-party applications, going forward. So 'avoid mucking about with third-party DEB and RPM files' is likely to become a rule of thumb for end users.