> It isn't. It falls slightly apart in the `s` column, and completely in the `t` column which contains both "chi" and "tsu".

All of this is described just below, in the section called “why romaji is actually bad”, with these specific examples being tested.

> It also breaks for godan words that end in "u" which become "wa" in the negative form.

This is also described further below in the post.

> as you frantically try to back-translate everything into romaji, but also removing excess w's and converting nda's as you go

I see “understanding the system” and “applying it fluently” as two separate activities. I find romaji more illustrative for the former because the system is phonetical on a sub-mora level. Whereas kana is more helpful for the latter. I don’t assume my reader is an idiot, and so I assume that they would be able to pick the right tool for the job on their learning journey. The fluency always layers on separately anyway, understanding doesn’t “help” there. It’s just that personally I find understanding a great motivator (and fallback) for developing fluency.