(Author here) I agree that methods like the ones you've described are indeed quite effective when executed successfully. I argued in the piece that this kind of process is often blocked on metacognition. That is: the reader has to regulate and monitor the processes you're describing while simultaneously grappling with new concepts. It's a lot to ask. And of course, the medium doesn't even explicitly ask it of the reader: when people do these kinds of methods, they're instigating that independently.
Even if we limit ourselves to just these methods, can't we imagine a medium which is somewhat more involved in the methods we claim are essential to understanding?
And if we accept that, one more provocation: wouldn't we want authorial intent to carry into the use of these methods? Given that the author is already carefully sculpting so much of the rest of the reading experience, why wouldn't we benefit from them extending their authorial direction to the metacognition around the book?