You are wrong in understanding the article.
Khan: Videos + rote exercises
Learning: Projects, complex problem-solving, exploration, argumentation, etc.
Dewey is worth reading.
Particularly in early mathematics and language acquisition (but also in most learning domains) you need both rote learning and exploratory learning. Fundamental concepts + exercises to build muscle memory are foundational to enabling students to participate fruitfully in meaningful projects, complex problem-solving, exploration and argumentation.
If you're flailing around without having memorized basic trigonometric identities, you're going to struggle severely to apply them to classical mechanics. If you can't do basic matrix multiplication, you're not going to build a graphics engine.
The article tries to damn Khan with an example about probing how neural myelination works. If you understand the foundations of electricity (by learning about capacitance and impedance) and have done some grueling foundational learning in organic chemistry, ready answers might spring to your mind. You need the former to make asking the latter fruitful or meaningful.
Khan deliberately uses the term "scaffolding" - which since we're throwing around dead education theorists harks from Vygotsky - which is precisely what a teacher provides by pantomiming elementary concepts for a child. Ultimately the child needs to internalize these basics to succeed in more complex projects with a sense of independence.
I really don't understand this article. Two things can be true at once.
Direct Instruction - and the largest educational study ever untaken Project Follow Through - would like a work. Project based learning?
Recall practice IS learning. Projects, exploration, and discovery-based "learning" sounds great in theory but in practice, without actual testing, really doesn't live up to the hype.
Adam Boxer is worth reading.