So, God can use disorder and chaos in order to bring judgement. So, God can be the author of chaos so long as he is bringing judgement to his world.
The flood was not chaotic or disorderly. It restored the order that was there before the sin of Genesis 6 and swept away the giants that were in the earth at that time.
All of scripture must be in harmony. All of scripture from Genesis to Revelation shows that God is not the author of confusion, lies, misery, etc. Satan is. The world in Genesis 1:1-2 was in a state of disorder and confusion, when God's Spirit hovered over it.
God did not author the world in a state of confusion. Something happened to make it chaotic. God didn't say, "Let there be chaos." That would be contrary to His NATURE.
I think I agree with that statement. Deluge, Babel, Destructive Fire, Blindness (maybe even Hell) could each be cited as examples of God utilizing disorder as means of judgement.
When Paul says God is not the author of confusion, maybe he's saying that God's people and godly activities are not characterized by chaos/confusion.
I'd say God can arrange any part of HIS CREATION in any way that looks to us like chaos from our very limited--through-a-glass-darkly perspective
any time GOD wants
for any purpose God wants
. . . consistent with His Nature, true--but FROM HIS PERSPECTIVE.
GOD IS NOT AT ALL bossed around by our perspective or constructions on HIS reality.
In case anyone hasn't noticed--it flows the OTHER direction.