Good question. I see you are not bothered by the idea of one person saying a blessing to another person. That is because when someone sneezes and we say, “Bless you,” we are really praying to God to heal the person who may be sick.
But clearly this cannot be the intent when we say, “Bless You,” to God, as you ask in you question.
The Hebrew word for blessing, beracha, is related to the word “bereicha,” which means “pool,” or more specifically, the pool into which the waters of a spring collect. When we describe God as “blessed” we mean that He is the ultimate “pool” of all that is good. He is the spring from which all of existence emanates. We acknowledge this reality by saying a beracha. We ask God to continue to pour forth His influence and His good upon us, and upon the whole world, because we want God’s presence and influence to be felt by every being in the world. Beyond acknowledging God as the source of all existence, a beracha is the means by which we reveal God to others and make His presence known in the world.