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The 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.

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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.
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Have you considered that different things are difficult for different people? Learning hiragana and katakana has taken me about a month, and I found it very difficult. There is no need to make it prerequisite for starting to learn grammar, forming sentences, or pronunciation.
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If you want to learn pronunciation you should be listening to audio.

Sure, maybe don’t force people to learn kana first. But Hepburn is kind of the worst of all worlds, it is just a waste of time to learn Hepburn.

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Notice how I didn't say that I "learned" both in a day, I "remembered" them. Of course actual learning will take some time, especially with less used characters. But remembering shapes and differentiating between them using mnemonics should not be too hard for most people.
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