No one is saying that the Son isn't distinct from the Father. The Father, a Spirit without flesh, sits on the throne of God.
Now, He was incarnated as the same Spirit in flesh, a distinct Person because of the hypostatic union.
This distinct Person sits on the throne at the Father's right hand.
And, He is the same Person come in flesh; and thus, He is a distinct Person from Him who dwelleth in eternity (Isaiah 57:15).
In that they are the same Spirit (1 Corinthians 12:4, Ephesians 4:4).
God the Father is a Spirit without flesh and the Son is the same Spirit incarnated in flesh.