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.