I'm suggesting that even to musicians, when they say, "I want to understand how music works", they pick up a book on "music theory". They think it does mean that. And they study it and hope it will get them what they want. It does a little. They aren't presented with the idea that any other approach even exists. And when they get advanced enough, some of them teach "music theory" classes and write more "music theory" books — all still thinking this is as good as we have at explaining the nature of music because they themselves sought that out and this is what they got.

At grad-school level "music theory" all the insights from music cognition are recognized as totally within "music theory" except that everyone is so invested in the general notation-jargon path to get there that they rarely think much about what theory could/should be for beginners. They eventually found the other stuff after so many years, and most people don't question whether there might be a better path.