alt Hacker NewsThe pair is something of a simplification, and romaji makes certain things in the language more obvious. Like the good old mat-u -> mat-anai, mat-imasu, mat-eru. Added the hyphen to make it clearer, but this hyphen splits a kana neatly in half. The stem is “mat” but you can’t write the stem using kana (in some sense of the word ‘stem’, maybe that’s not the correct word and there’s a different word for it, I’m not a linguist).
I’m not trying to say you should avoid kana, just that there is some amount of intuition you can develop with romaji that does not work in kana.
The traditional way to develop a similar intuition with a kana-only approach is to think of it as "moving across the row" in the kana table, which works fine. I think the fact that with romaji we can represent the stem as mat- is interesting and valuable in a theoretical sense but not all that useful to a learner.