This seems to be overlooked by far too many people. If the kind of confusion you see regularly on this forum is any indication acquiring theory without the guidance of an experienced player causes at least as many problems as it solves. Inexperienced players trying to "apply" modes over chord changes is a classic example. Sure it works mathematically but honestly superimposing modes over chord changes has never made much sense to me musically. I was taught the Berklee modal system in my late teens but right away I realized that taking it too literally didn't always sound very good. Fortunately I had some good teachers who didn't let me loose sight of the fact it's musical theory not musical laws. Another thing I think gets badly overlooked is that trying to learn theory from what you can hear on an instrument like the bass which functions primarily using single note lines makes it incredibly difficult to gain any real depth of practical understanding of harmony.