Actually let me just try to explain my pedagogical approach and philosophy here. Maybe that makes it clearer.

I assume no prerequisites at first. So my reader has never seen a kana table and doesn’t know which syllables exist.

I choose to teach conjugation first. That’s an unorthodox choice but I like it! That’s what I set out to do. So we get far enough until it breaks down. And it breaks down when a rule (which worked so far) doesn’t help with “s” because saying “si” would sound wrong.

That’s the moment I use to teach kana table and its importance. This “you made a mistake” is a pedagogical vehicle for introducing kana rows. And we go over the exact ones that you’d make a mistake with. So each special case is walked through.

At this point we could discard Hepburn but I choose to keep going because if you know special cases, there’s no issue. And at some point you’ll learn kana anyway.

So that’s how I chose to layer it. Maybe it’s a bit unholy but I like it. It is definitely self-consistent.

I understand why you wrote the article this way, I think the lesson here is “we have learned why Japanese textbooks do not teach the content in this order” and there are a couple reasons why this order is not good:

1. It relies on people not understanding certain things. In general, you cannot expect people to have exactly the right misunderstanding necessary for a lesson.

2. Spending extra time with Hepburn reinforces it, and it shouldn’t be reinforced.

I am in general extremely skeptical of lessons which try to engineer a way for the students to make mistakes. What I have seen in real classrooms and in informal teaching is that the mistakes are habit-forming and the outcomes of this kind of engineering are unpredictable.

Mistakes are appealing to the developers on HN because we understand things more by seeing them fail. But this does not mean that you can engineer somebody to experience the same moment of enlightenment that you did, because it requires constructing the same (incorrect) mental model that you had when you made that mistake that led to useful insight, and it both difficult and counterproductive to try and make that happen to students. Give people the best chances to learn by giving them the best chances to avoid mistakes, and the mistakes and insight will happen organically on their own, in unique ways for each student.