"Music theory" has a near universally accepted meaning. This article is not about that, it's about what we all call in music academia acoustics and digital synthesis (which of course I know you know as I know your work). The derivation of scales from acoustic principles is not in theory books; it's in acoustics books. I've taken numerous theory courses and also taken university acoustics courses and digital synthesis courses, so I can certainly comment on what was taught where! If people go here and think they are learning music theory and then want to go on, they will be frustrated by not finding what they want, they will have issues communicating with others in the field, and they will lose credibility by not knowing the standard nomenclature. That kind of redefinition of standard terms is not good pedagogy.
Look, it's like me writing an introduction to "colour theory" and then writing about something else that eventually leads to how we see colour.
I'm not debating that the article has useful content – it does – but it's title and framing is misleading, which is a disservice to the new student. I happen to personally believe everyone getting into music theory would be well served by knowing more acoustics and that this is useful material. But muddying the waters by using terms in weird ways is off.
And when you write about a field and use the wrong terms, you lose credibility. Sorry, I don't trust authors who can't be arsed to use the standard nomenclature for a topic, it really doesn't make them sound trustworthy.