I'm a little puzzled in what way the male student misunderstood what the MC was teaching him.
It appears to me he was explaining that there was a lot of depth to even basic spells, and 'mastery' is a vague term, which the kid seems to get.
... Or is both the kid, and myself, misunderstanding here?
The misunderstanding was how Kunon thought anyone could do what he does. Making your A-Ori take the precise shape, and variegated colors, and exact temperarute of a cow head is a genius technique. But Kunon tells him that it's easy, once you master A-Ori. Now Glyph is going to struggle to figure out how Kunon did it, and oh boy, it will be a struggle.
To piggyback on this, I think this was a particularly deep chapter on educational philosophy. Part of what Kunon was saying is that a spell isn't mastered by doing it one exact way, but by figuring out all the different ways you can use it. Contrast that to our modern educational system, which was designed to teach people to do factory labor or bureaucratic work exactly the same each time. Kunon's way is creative, and encourages individuality, and leads to new ways of thinking and doing. That is, progress. But trying to do something exactly one way leads to stagnation and boredom and frustration.
The other side of Kunon's philosophy is that not everyone can be as creative and individualist as he is. I bet Glyph will take his challenge and work himself to tears. He probably becomes an above-average A-Ori caster. But will he ever match what Kunon can do with it?
One last idea is that Kunon just showcased the inductive and deductive reasoning styles. Glyph saw a dozen different high-level spells, and will need to figure out the single 'mastery' or A-ori from there. Lim saw one high-level spell, and will need to try a dozen different methods to achieve it. Top down versus bottom up design! Both are ways to achieve Kunon's type of mastery, and the two different students could find one method is better than the other. I assume the author showed us these two students for a reason, and we're going to get the eventual 'results' of Kunon's unintentional educational experiment.