To work around this problem, please add a unique string to the Universe container that none of the users have access to. This also applies to any container that is shared by users, who don't have access to all elements, in the container. This will remove the topology view of the universe, from all but Admin users, or users given the unique string.
Users can still see their containers in the Explorer tab and navigate via the topology view below the universe level.
The documentation has been updated to include this.
Please note, that until the above steps are in place, all users will be able to see all other users' containers, in the topology view, but they cannot access them. Each user still only has access to his own container.