I would like to propose that the darkness doesn't come from our universe but from another dimension. One of the darkness cards suggests that in theory, our universe is made of atoms because in the battle between atoms and the primordial broth, atoms won the right to exist, and henceforth our universe is made of atoms and follows atomic physical laws. In theory, if there were an alternate universe where atoms lost the fight, then the universe would be made entirely out of something else, and wild follow the physical laws dictated by whatever else that thing was that won. The darkness probably comes from such a universe, and this is why he is able to employ paracausal weapons (weapons that alter reality) so easily in our universe.