Snapshotting is never going to be an atomic operation, this is a false argument for unified /usr. What happens if a package is being installed when the snapshot takes place. e.g. parallel installation of a tarball by someone else. If you roll back you end up with something half installed.
So you have to procedurally "quiesce" the system FS to avoid race conditions. Given that, what's the difference between snapshotting one FS or 3,4,5,etc?
The only reliable way to manage the system is to use the package manager to undo the changes as it currently does. And if this is not possible, because the system won't run the package manager. Shame the sys admin who broke it for being so careless.