I find this discussion a little saddening, since I think that what he's talking about here was not really present in The Witness (and I loved the game, don't get me wrong).
I feel like the primary way he achieves epiphany in The Witness is by not giving any explanations for the puzzle rules, and yet in the game you constantly have rows and rows of tutorial puzzles at your disposal thrown right into your face every time you go to a new area. I don't think you "actually have to be smart" to figure out the rules when they are given to you in such an obvious way. You may as well have included the tutorial text, the very thing you didn't want to include!
The music box challenge might be the first thing people respond back with, saying "Well that challenge is certainly very hard and you have to be smart to solve it!" I disagree. That challenge is heavily reliant on RNG. You can pass it given that you're willing to try over and over again until you get easy cases. And often, when the cases aren't easy, they go off the deep end and are very hard (usually because there are blockages everywhere), which makes it a no-brainer to restart the challenge and try again. The music box challenge sidesteps epiphany in favor of brute force repetition until the RNG is favorable.
I like how Blow thinks, but I also feel that he spends more time in his own head than he does applying these principles to his games. The theater itself is a prime example of this, and it reminds me of how the writers of LOST treated their franchise. Naming characters after famous philosophers and scientists while throwing in books at various points doesn't mean your story is profound. It's almost like they try to be "deep by proxy," as if name-dropping all the time is enough to lend the thesis credit. The theater in The Witness does this as well. The audio tapes, the lectures in the theater... much of it is interesting, but none of it actually drives anything forward. It's all just "there." Science and philosophy is cool as long as you can actually tie it into your game. And if the idea is to go "meta" by saying that this game's purpose is the game itself and the experience you have playing it, then there are much better ways to get this idea across without the heavy-handedness.