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?