3. The principle of all sovereignty resides essentially in the nation. No body nor individual may exercise any authority which does not proceed directly from the nation.
Article 3 of The Declaration of the Rights of Man.
That is not talking about sovereignty as in whether God is sovereign over man. It's dealing with whether political subdivisions of France can exercise sovereignty. Remember, France is one political unit, it is not composed of smaller sovereign states.
Up until Louis XIV's reign, various regions of France exercised a lot of sovereignty. This provisions is stating that such behavior is no longer acceptable. This is a purely political provision.