I think you're missing the point, Atenolol. We can't understand the method they are using, because they are more advanced than us. A dalmation doesn't understand what humans did to make him different from a collie, but it was still done by natural means.

We watch Bowman take the next step in human progress at the end, and there's no evidence of mysticism. Did anything in the light journey look like a mystical intervention of angels to you? Are you saying that the "time mirror" (whatever that is) in the room at the end was somehow outside of science just because you can't explain it? Did you see the hand of God reshape Bowman into a star child at the end?

You see mysticism because the events are outside of your experience. I'm postulating that that's a somewhat primitive reaction to the movie, just as the Pacific Islanders forming cargo cults in an attempt to lure back WWII aviators after the war had only a primitive understanding of western technology.

The why and how of the aliens' intervention in 2001 are never explained. But that doesn't make them magic.

But as I said, you can see it that way if you want to. I don't, and it isn't due to my fondness for the movie.