[dnanian]

Those folders weren't changed, and since they're not shared, any changes made while running from the Sandbox will not be reflected on the original volume.

That is - shared files (eg home folder items) are changed on the original volume, when you make changes, because they're linked to the originals. Those root folders are on the Sandbox, and would only be updated on the original if you were to copy back, as explained in the User's Guide.