This is a profound mystery—but I am talking about Christ and the church.The author is bouncing back and forth between the two topics: Christ and the church, husbands and wives. When relating the quote from Genesis, speaking on the one-flesh relationship of husbands and wives, the author pauses to mention that it is a "profound mystery" or a great mystery. The word mystery comes from a word that means to "shut the mouth." It is used by rabbis when referring to some O.T. saying that has a hidden meaning.
God is never pulling things together at the last minute. There might be some stuff that is a mystery to us, but it is simply because God has not revealed it to us. There is nothing that is a mystery to him. In fact, as He reveals new things to us in the New Testament, we find that He had things planned from the beginning.