>the explanation here is misleading

Misleading means it leads to a wrong conclusion somewhere. Please demonstrate which wrong conclusion my article is leading to.

>and that's because of the dependence on romaji / transliteration

There is no "dependence" on transliteration per se. I use it as a visual shortcut for moving along the kana row, as I show in the middle of the post using the table. For all the examples we're looking at, the relationship between the mora and the corresponding romaji version is bijective — so there is literally no difference except the notation. I wanted the article to be accessible to someone who's not fluent in kana (and in fact to someone with zero knowledge of Japanese), hence the choice of notation.

>First, there is a clear stem (飲＊), but you just don't know that yet, because you haven't learned kanji

What could kanji possibly have to do with this? We're discussing a thing rooted in phonetics. The verb stem often includes kana in addition to kanji (e.g. 食べ). There's nothing special here about kanji at all.

>To wit: a godan verb [2] shifts from the "u" sound [...] to the "i" sound in the same column of the kana table [...] Then, for casual negative conjugations, you shift to the "a" sound in the same column

Sure, and that's exactly what I'm describing in the article. Why do you need to pretend I'm describing something different? There's even a place in the article where we use the kana table for that. However, since I assume the reader might not want to constantly look at the kana table, I focus on the phonetic intuition. And the phonetic intuition is trivially explained with romaji, which is why I use them.