This is the way that the Bible has laid it out. The Trinity is a concept that is derived from the Bible to give is a glimpse of the totality of God. We, as finite men have no real idea of God in his fullness. The trinity is just a hint. In the Bible God has said in different places and ways that there is only one God but the one God is the Father, the Son and the Holy Spirit.During Saul's conversion why call Jesus God the Son when he is God manifested in the flesh and in "him" dwelleth all the fulness of the Godhead bodily? Is "him" also called God the Son? Where is the Father and Holy Spirit during Saul's conversion?
Jesus, for our ability to comprehend God, is the Son of God, God in the flesh and in him dwells all the fullness of the Godhead bodily. That is a fact whether we can understand it or not. In the sentence you seem to be quoting, him is Jesus, the Son of God. God is present in Jesus and therefore the Father and the Holy Spirit are there as well. God can be everywhere at once without limits.