Every element of Western music builds on the same building blocks. Western harmony, as taught, relies on understanding chromatic and diatonic harmony; the author did a nice job figuring out and explaining the compromises inherent in equal temperament (without knowing about how ratios and tuning worked before equal temperament; people didn't always fudge the ratios to make them work out the same across all keys), which is cool. But, he still doesn't actually know much about western musical harmony, as evidenced by the assertion that C Major and A minor are "the same", because they share a key signature and the same notes. Had he known that equal temperament is a moden-ish invention, he might have also figured that C Major and A minor actually have (slightly) different notes if your instrument is tuned specifically for that key rather than with equal temperament.
In short, he's just not done learning yet. Most musicians and composers never really are, as it is a vast subject. And, what he's calling "music theory" is really more "equal temperament tuning math" with very little theory.
Not to say it's not interesting and well-presented. It may be useful for non-musical nerds to see it presented in this way.