I haven't read the whole text at the link (for which I'm grateful) yet, but I'll comment on the quoted paragraph.

I feel that music theory has gotten stuck by trying too long to find universals

More specifically, however, the problem is a confusion of universals with fundamentals. Music theory has succeeded in finding universals, but such universals by themselves aren't explanatory. If you don't know how to compose, it won't help you very much to learn that ancient flutes play the diatonic scale. And if you start doing statistical frequency analyses of local musical behavior patterns in some specific repertory, you've utterly gone off a cliff as far as explanation is concerned (at least, the kind of "explanation" that is of relevance to a prospective composer).

Music theory, as a discipline, suffers from a failure of query-hugging. My belief is that if theorists were to engage in honest introspection, they would, at the end of a (possibly quite long) chain of inference, reach the conclusion that their real goal is to devise a "programming language" for music: a set of concepts that facilitate the mental storage and manipulation of musical data. And that, if they attacked this goal directly, with conscious knowledge of what it is, music theory would (a) look very different (or rather, look a lot more like certain existing theories than others), (b) be more intellectually satisfying, and (c) be a lot more relevant to musical composition and performance.

(I'm grateful to Daniel Burfoot for the "programming language" metaphor.)

But we must view these with suspicion, for they might show no more than what composers then felt should be universal. If so,

I'd be surprised if most composers were aiming at universal music. I would expect them to be trying to create music which would move their audiences and themselves, and sometimes just the former.