Maybe the magic is in the artist dedication from early age to developing and honing the skills required to create non reproducible works, works that we want to be deceived by.
The masters cited in the video, particularly Da Vinci, were genius masters of their craft who studied under previous masters (Da Vinci under Verrocchio @ 15). Some masters operated schools in addition to having apprentices who would help with the paintings (or sculptures). If metaphysical practices were employed to produce these works then it was highly known and I suspect would be part of artistic education today. Remember that masterpieces were being produced in more than just Italy so that knowledge would have been disseminated. Perhaps some of the artist were alchemist (evidently not-an-artist physicists Newton was) but that was in addition to being masters of their craft.
I've seen almost all the pieces in that video in person. I'm the guy setting off alarms by getting to close. And I somewhat disagree with their assertion that brush strokes aren't visible. Go to a museum and look at the paintings and you will see brush strokes at least occasionally, maybe not on the Mona Lisa but you're only allowed to get about 3 meters close so I don't know. Mona Lisa is a masterclass which can't be summed up quickly but youtube has some amazing breakdowns.
I have seen some pieces still with pin holes where string for perspective was used over the course of the work but there are lots of techniques for perspective.
You've probably already been but if not, go to Rijksmuseum there in Amsterdam. It's great especially if you are a fan of Rembrandt.
Also, Isn't the philosophers stone theoretically for transmutation of base metals into gold?
