Yet another case of programmers thinking "I'm a programmer so I should blog about this thing I barely know anything about as if I'm an expert, what could possibly be the downside?"
There is "western music theory" ala Schenker, voice leading, serialism etc (to mention a couple of names that some people might have heard of) but that describes things to do once you've got a scale and chord system.
This is "12T music theory", describing how you might get to a scale and chord system.
I don't see how it is confusing. You can spend a lot of time doing "western music theory" without ever understanding most of what is in this article, that is certainly true. But the fact this this outlines a bunch of stuff that undergirds what a composing (or improvising) musician might consider "music theory" doesn't invalidate it, or make it confusing, IMO.
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.
Scales and chords build the fundamental basic blocks for Western music (I would introduce equal temperament third but that's only a matter of ordering). They are taken for granted in musical practice, I agree, but only because musical practice concerns itself about how/what to play and why. If somebody comes from the point of view that clefs and stems (which are undoubtedly musical tools) are gatekeeping and all you need is a piano roll, this article explains from first principles enough musical building blocks to tell them why they're wrong.
On the other hand, if the author had said something like "Intro to the acoustics behind musical scales", then they might go on to order great books like Kyle Gann's or Gareth Loy's and be off to the races.
Redefining normal terms just makes people sound like they have no clue, and that is, 100%, a serious disservice to the reader/student.
Harmonics and temperament aren't really relevant to all this, though at some point you have to explain why certain intervals are naturally consonant but "boring", and others can be made to make sense but mostly within a more complex voicing (which reconnects to topics like inversions and voice leading).
(For disclosure I studied piano until ~20, both classical and jazz, and I would call my knowledge of jazz theory "decent" for someone with zero professional or academic experience. Obviously not comparable to yours and not even in English, so perhaps what I wrote above will sound really stupid).
And this is correct because ... ?
There are whole subsectors of "music theory" that cover precisely this sort of thing, even though they are fairly arcane. I'm thinking of things like pitch set theory.
My own take is that western musical pedagogy, at least historically, is one of the worst examples of pedagogy that exists, precisely because of what is taught, in what order, and why. It pretends (or used to) to have some sort of universality or inevitability, when even a scant familiarity with other musical cultures would make it clear that this is false. It is emphasizes a note-centric rather than interval-centric approach to melody (and chords) that ignores centuries of (folk) musical practice (most simply known as transposition, but the implications of it are staggering, and largely elided).
So, defending what that pedagogy calls "music theory" seems like weak sauce to me. Especially given, as many others have pointed out, western/european "music theory" is a codification of existing practice for the most, not a generative theory.
Whether or not this info should be in acoustics books or theory books is not relevant to the new learner, that's where it is! I actually think a crash course in acoustics would be a good addition to a comprehensive theory book, but it doesn't change the fact that no theory course or book has this stuff (not even my pitch set texts!)
I teach music students regularly. I spend a lot of time explaining what something is called in various contexts. They need to know this to learn in a productive and not frustrating manner. They can then learn later why the terms are imperfect and used differently in different subcultures.
But no argument on that is going to convince me that it's good pedagogy to tell new readers that a post on acoustics and synthesis is on music theory. That's just counterproductive at best, or ignorant at worst.
Look, I agree that they should be. I have literally had discussions with one of my PhD supervisors (who taught acoustics) about how much better some students would understand some of harmony if they started with some acoustics! But they aren't, so if one is going to redefine common uses of terms, at very least this should be explained in detail to the student prior to use.
My call on this stuff is always determined by "What will help my student learn most efficiently, without frustration or confusion". That article fails badly on that count.
The example I'm most familiar with is Carnatic and Hindustani music, where there are theoretically 22 tones per octave, and in fact the tones in most cases actually cover a range of frequencies rather than a single one. Nevertheless, the most common and most popular music from those traditions tends to only use about 7 tones per octave (equivalent to a western "scale"), and they still have a very central for tone ratios like 3/2.
The point is to make music. And the most practical way to do so is to teach instrument technique, intervals, scales, chords, and melody. Not low-level acoustic phenomena.
To make an (imperfect) programming analogy, you are proposing to teach low-level computation when most students would benefit from some Python, if/else statements, and functions. Not memory allocation and assembly. They're useful someday, but less useful when your first goal is to simply write a program.
Is it? Why?
If you have an alternative reason to learn music and to start learning through acoustic phenomena then let's hear it.
Most people don't get into molecular gastronomy if they don't intend to cook a meal. And I'm going to go out on a limb and say that 99% of aspiring cooks shouldn't learn cooking via that discipline without first starting with something more practical and immediate.