It's long been interesting to me that the Wackowski's inverted the relationship between The Architect (the demiurge) and The Oracle (Sophia) according to Gnostic myth. That myth says The Logos (Neo) and The Oracle (Sophia), or truth and wisdom, are responsible for The Architect of this present Matrix.
But yeah, I do share your view on the absurdity of it all.
A coherent theistic view to me is that we are God dreaming! We all know how absurd dreams are!