The reliable illusion in learning is that following an explanation feels like understanding it. It is not the same thing and it does not feel different from the inside — which is why people re-read a chapter, feel it click, and then cannot use the idea a week later. The only thing that separates them is being asked to produce something rather than recognise it.
The three depths exist because a single explanation is always pitched wrong: too simple and you get an analogy you cannot use, too detailed and the vocabulary arrives before the shape it is describing. Reading the same thing three times at increasing resolution is close to how the idea actually settles. The layer people skip is the third one, and it is the one that matters most, because the simplified version you were given is wrong in specific ways and knowing which ways is a large part of knowing the subject.
Phase two is the point of the prompt. Four of the six questions are about applying the idea somewhere it was not explained, which is the only kind of question that can distinguish having an idea from having its vocabulary. The final assessment is instructed to be blunt for the same reason.