But if his human nature is not present, wherever his Godhead is, are not then these two natures in Christ separated from one another?

Not as all, for since the Godhead is illimitable and omnipresent, (a) it must necessarily follow that the same is beyond the limits of the human nature he assumed, (b) and yet is nevertheless in this human nature, and remains personally united to it.

(a) Acts 7:49 Heaven is my throne, and earth is my footstool: what house will ye build me? saith the Lord: or what is the place of my rest? Jer.23:24 Can any hide himself in secret places that I shall not see him? saith the LORD. Do not I fill heaven and earth? saith the LORD. (b) Col.2:9 For in him dwelleth all the fulness of the Godhead bodily. John 3:13 And no man hath ascended up to heaven, but he that came down from heaven, even the Son of man which is in heaven. John 11:15 And I am glad for your sakes that I was not there, to the intent ye may believe; nevertheless let us go unto him. Matt.28:6 He is not here: for he is risen, as he said. Come, see the place where the Lord lay.