Not at all. OS packages run scripts as root during installation, and this is why you should install software only from trusted Linux distros. Sandboxing user a

Not at all. OS packages run scripts as root during installation, and this is why you should install software only from trusted Linux distros. Sandboxing user applications is a completely orthogonal topic. You can sandbox OS-installed applications or other applications. With the same tools. Both options equally require custom configuration depending on what files and directories you want to allow or restrict access to (and syscalls and so on). Fine grained permission are a personal choice and both firejail and nspawn make it quite easy to configure.