When someone says that God is Sovereign, any Christian worthy of the name finds himself agreeing but at the same time feels that the speaker is using code for something else. It is largely because the idea of YHWH, maker of Heaven and Earth, being sovereign is too obvious to be that speaker's only motivation. He who intones that "God is sovereign" is "up to" something. The word "sovereign" means "rule" and, of course, God does... all things. But the person that was belaboring the obvious was not saying that God rules, he was saying that God exercised a certain kind of rule, that of exhaustive sovereignty. He is saying that God is an Autocrat (all decision falls to Him) versus a Monarch (the highest and ultimate judge of all decisions).
The foregoing is an example of the infamous "boa constrictor" argument. This a form of argument is one in which a concept is uttered in terms with which everyone in the audience will agree (the loose loops of the snake) and once everyone assents to it, applying it narrowly, presuming on the agreement of the audience (constricting the coils). It will either be that the loose or the tight use is being misdefined. In this case, the tight is the erroneous usage.
They say, "God rules."
We say, "yeah, you betcha."
They say "So you agree that God is in exhaustive control and has decreed all things."
We say "Nope."
The question before Christians regarding the Sovereign of the Universe is His method or kind or extent of rule. And the debate is narrower than we think. The nature of rule is that there be two (minimum) participants, that which rules and that which is ruled. They don't have to be outside an individual as in the mind ruling the body but they must be discrete. The discreteness is present only if there is a real potential of regard and disregard of the ruler. The ruled may not merely be the extension of the will of the ruler or there is no other will for the ruler to rule. If God's governance is presumed to be an exhaustive autocracy (in which nothing occurs but the will of the ruler) there is no actuality to the existence of the party called "the ruled". We know that in ourselves, that the closer we get to an absolute submission to our wills, the more closely we are able to define that which is our self. If there is an absolute and exhaustive submission to the will of God, nothing exists but Himself. The apparent diversity of creation would be merely the presence of God. It is pantheism ( "God is everything and everything is God … the world is either identical with God or in some way a self-expression of his nature"). Consequently, exhaustive divine sovereignty is not sovereignty at all. Only that which grants (by whatever method) an encounter with possible obedience and disobedience can claim to rule. God rules like all rulers rule. He has not exhaustive decision but exhaustive imperium, the unquestionable ability to reward and punish all things. His absolute ability to punish and reward all that is in His creation is the arena of sovereignty. The question before Christians is between, and the ratio between, that which He causes and that which He rules.