I don't know squat about tracking - but still, I have theories...
My understanding is that tracking requires extensive knowledge and understanding of the environment and ecology - not only the habbits and preferences of whatever you're tracking, but also the habitat, plants, other animals and how they affect each other. Not in books, but in the actual environment.
This takes A LOT of time and practice. I have no trouble visualizing how the thorogh ecologic understanding will come close to having "mystical" qualities. It is just how the mind works: Yearlong experience is distilled into an intuitive understanding of what's going on in the woods today, what those faint marks in front of you are, who made them and why.
I don't see mystery. I just see a thorough understanding of a complex ecosystem and fine honed set of skills - knowing what kind of marks to look for and why.