I think that’s a long wait; I don’t want to rely too heavily on analogies but it is like teaching somebody arithmetic roman numerals and then explaining in a parenthetical that there are other ways to do arithmetic (but not naming them). Maybe the reader can make up their own mind—but I don’t think the pros and cons are raised in the article, or if the are raised, I couldn’t find it.
I don’t want to pile on here but it sounds like you are, in this conversation, learning about why the different romanizations exist and what the pros and cons are. Or if you already knew, you are getting what they call an object lesson. (Like you noted—in Hepburn, ji and zu correspond to two different kana each.)
> As I noted somewhere else, you could imagine that I’ve chosen IPA notation instead.
This just resurfaces a similar problem with different symbols—if you put your IPA notation in slashes // you get phonemes, which will get you something mostly equivalent to Kunrei-shiki romanization. If you put your IPA in brackets [] then you get something sort of equivalent to Hepburn (in that it’s designed to show pronunciation). Both choices will on some level obscure a regular pattern that could be revealed with kana or romaji. Orthography is funny like that; in both Japanese and English it can show the origin of words even when the pronunciation changes.
I think the other lesson here is that students will mostly learn morphophonology intuitively by absorbing examples with some light explanations of the rules, and if you overexplain the rules you end up with too much “scaffolding” which gets in the way. Like when people use mnemonics or try to memorize kanji by thinking pictorially.