> Work on large systems long enough and immutability becomes a very valuable concept.

On the other hand, if you work on medium-sized systems (and those are much more common than large ones), immutability is too expensive to work with.

> Installing application dependencies when each server starts up increases the chances of servers running different versions of packages

Only if you're stupid enough not to package your dependencies, if you use distribution not suited for servers (like Fedora or Ubuntu non-LTS), or if you use external repositories you don't control that don't have stable retention policy for packages. And mind you, these three were always a bad idea. Appearance of Kubernetes and other magic faerie dust of Docker haven't changed it.