Has there been a shift in Christian metaphysics from a unitary cosmos to a binary one? It seems to me that before the Enlightenment, the predominant understanding of the structure of the universe was that the cosmos, while stratified, is unitary- that "the Heavens", which include the spheres of the stars, then of the angels, and the abode of YHWH, have substantial existence in the same way that the Earth does.

An example that this belief was commonplace is Pauls refusal, upon describing an event in which a man "went up to the third Heaven" in 2 Corinthians 12:2, to say if he went up in the body, that is physically, or in the spirit. 

It also seems that after the Enlightenment, the predominant understanding of the structure of the cosmos became binary- that there is a physical realm of existence and a spiritual realm of existence, where the spiritual realm both fills and transcends the physical. 

Is there historical evidence to suggest that such a transition has taken place within Christendom?
It seems to me that before the Enlightenment, the predominant
  understanding of the structure of the universe was that the cosmos,
  while stratified, is unitary- that "the Heavens", which include the
  spheres of the stars, then of the angels, and the abode of YHWH, have
  substantial existence in the same way that the Earth does.


When one speaks of Christian beliefs, one must recall that the beliefs which developed in the west - particularly in the medieval period, perhaps beginning with Charlemagne - were in some cases radically different from the beliefs held by the eastern Christians that now, for the most part, form the Orthodox Church.

I don't think any of the Church Fathers had a belief that the abode of God and His angels had any kind of "substantial" existence.

John of Damascus (8th century) explained:


  The heaven [sic] is the circumference of things created, both visible
  and invisible.  For within its boundary are included and marked off
  both the mental faculties of angels and all the world of sense.  But
  the Deity alone is uncircumscribed, filling all things, and
  surrounding all things, and hounding all things, for He is above all
  things, and has created all things.  For the great part the
  heaven is greater than the earth, but we need not investigate the
  essence of heaven, for it is quite beyond our knowledge. 
  -- An Exact Exposition of the Orthodox Faith, Book III