I wonder if this could also be used on immutable distros as a way to make temporary or even semi-permanent changes, like installing a system-level app such as a VPN (I ask because the built-in layering solution on distros like Fedora Atomic isn't ideal).

Assuming there is a use case for immutables, what I don't understand is the "sync" business - if the overlay sits on top of the host and sees the host's files, why does it need to "sync" exactly? So say I have an app installed in the sandbox, and I upgraded the OS to the latest edition—what would be the behaviour in the sandbox, and what's the best solution for that? Like, do I need to even run a sync in the first place, if I rebooted the machine? What does the sync do exactly in this instance? And I'm guessing any changes made inside the sandbox would get overridden? Say the app modified /etc/resolv.conf in the sandbox, would a sync override that file? Would the best solution be to reinstall the app(s) in the sandbox, or delete and recreate the sandbox and then reinstall everything inside? Probably best do this on every boot then I suppose, via a script or something?