The problem is that your explanation confuses phonemes with letters.
A spoken language is described by decomposing the spoken words into phonemes, where phonemes are sounds that distinguish words, in the sense that replacing one phoneme in a word with another phoneme will produce a different word.
While ideally each phoneme should be recognized by a distinct pronunciation, in the majority of the languages of the world a phoneme does not have a single pronunciation, but it is pronounced in different ways, depending on the context.
It does not matter at all how one chooses to write a Japanese word, with hiragana or with one of the various methods of romanization. For any writing system, you must know the correspondence between phonemes and how they are written. For very few writing systems there is a one-to-one mapping between phonemes and letters.
The Hepburn romanization does not attempt to be a phonemic writing system, but it attempts to be close to a phonetic writing system from the point of view of an English speaker. The Kunrei-shiki romanization attempts to be closer to a phonemic writing system than to a phonetic writing system. I my opinion a phonemic writing system is superior to a phonetic writing system, but it appears that for most English speakers it has been too difficult to understand the difference between such writing systems, so the Japanese government eventually gave up and they switched to Hepburn, to please the less sharp-witted English-speaking visitors.
Japanese has an "s" phoneme, which happens to be pronounced differently before the vowel "i" than before the other vowels, and before "i" it is pronounced similarly to an English "sh".
In the same way, the Japanese phoneme "t" is pronounced before "i" similarly to an English "ch".
Once you know these two rules, and the few other rules about the other Japanese phonemes whose pronunciation depends on the context, like "n" becoming "m" before "b", there is no point in mentioning them again.
In your discussion about conjugation there is nothing exceptional about the variations in pronunciation that are reflected in the Hepburn Romanization. They are just the general rules of Japanese pronunciation, like for any other words.
So any discussion about these spelling variations is misplaced in the discussion about conjugation, where it occupies a space without contributing anything to the understanding of the conjugation rules.
Otherwise, I think that your article is fine.
I get that. I’ve compressed this as an aside in an article about something else. It’s a choice; like an article about React could spend a bit of time on arrow functions vs function declarations as a choice. Or even let/var. It all depends on audience’s prerequisite knowledge and what you choose to assume.
I strongly suspect that if I were using Kunrei-shiki, there would be just as many comments here saying my article is wrong because “si” is pronounced closer to English “shi”, but my article makes it seem like it doesn’t — so this is why you should learn kana bla bla bla.
I assume my reader (1) has zero prerequisites and (2) wants words to sound correctly while seeing them the first time. Those are the constraints that motivated my approach. You could argue that it’s a strange set of constraints to pick when teaching but I wanted it to be fun.