That's true, but if you take the "observed phenomenon" to be "Western, common-practice tonal music (and notation)," then this certainly helps to explain it. It's certainly what gets taught in undergraduate music theory classes (much of it in "fundamentals" courses). Graduate work in music theory involves doing exactly what you say: explaining observed phenomena, in both "classical" music as well as about any other musics you might imagine. That's not to say that all music is Western, common-practice tonal music, but a great deal of music comes out of that lineage; an understanding of these basics are often necessary (or at the very least, useful) before branching out.
You see this sort of thing in all disciplines. I might find an "Introduction to computer science for normal people" that explains big-O notation, or teaches some basic Python, or what have you. Someone might well say "This isn't 'computer science,' but instead 'jargon and programming.'" This person might be right, of course, but for "non-computer scientists and normal people," the distinction is not so clear.