Your question has nothing to do with God, so I'll just leave him out of this. So, magic or QCD phase transition? Well, since 'magic' means that stuff we don't understand caused something to happen, obviously magic is the most correct answer. It also isn't an answer at all--which is why it is good that people are exploring other ideas for the origin of matter. Your link wasn't very conclusive, but looks like a thought in the right direction.
By the way, do you think that thoughts are real? I find that people looking at a tiny corner of 'magic' often forget how much of it is out there. A lot of people think that explaining a miracle makes it less miraculous, while I'd strongly disagree. My studies have been more focused on biology than physics, and the more I see how things happen, the more miraculous they seem. Getting rid of the magic doesn't get rid of the miracle--it just tells you how it was done, like one of those TV shows exposing an illusionist's secrets. It doesn't make the illusion less entertaining--you already knew it was an illusion before you saw it--explaining how or remaining baffled doesn't make it 'fake' or 'real'.