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.