Well your first instinct is the right instinct. All of reality was indeed made by the Lord God Most High. It is detailed variously in the Bible and especially in the opening chapters of Genesis the nature of the reality which is called Creation. There is no parallel universes, there is only the one which God made.
As for the so-called "spiritual realm" that does not exist either. Creation is a big place, everything the Bible describes from the earth, the heavens, the valley of the shadow of death, the treasuries of hail and snow, and so forth are fitted somewhere in the Creation as the Lord God designed. As for the fallen angels, they are still around and in the Creation to boot, they are not in a "spiritual realm", they are below your feet even right now down in hell. The Apostles Jude and Peter make plain that the ancient fallen angels, because they forsook their first habitation, are now bound in darkness in everlasting chains until the judgement day.
No, I think rather than any sort of grand conspiracy to do with fallen angels that this is simply yet another case highlighting the atheists and their typical errors which are rooted in their fundamental inability to accept or understand the Bible and reality, particularly cosmology. The atheists have created their own cosmology and history which is basically in totality against the Bible. Again, I suspect it to be a sort of psychological escapism. That is to say they are trying to escape Biblical reality by denying the existence of the Creation as described in the Bible and instead have made up their own cosmological model as a means to deny the Creator and in their minds escape from the reality of the creation laid out in the Bible and thus to escape from believing the Lord God. Ironically not only do they have to escape reality by crafting a fantasy, but even their fantasy is flawed and they have to try to escape from their own fantasy model which is not real, by colonizing other earths which simply do not exist, by making contact with aliens which do not exist, by drawing resources from parallel universes which also do not exist, and so forth and so on. They're not going to go anywhere, they will never escape the hand of the Lord God.
To paraphrase the prophet Amos which prophesied the word of the Lord; "if they dig into the depths, my hand will take them, if they climb into heaven I will bring them down."