They have totally different goals.

Music theory is descriptive, not prescriptive. Oodles of people make music without knowing a lick of it, and people who learn it in academic environments still typically make music starting from other concepts. "Listen to records and vibe with what they are doing" is typically a much more effective way of learning to improvise seriously than "learn the theory rules", for example.

"Music Theory" also typically is very tightly bound to harmonic analysis modes that are focused on about two centuries of western european music. This is necessarily going to limit its effectiveness when applied in other spaces (even here, when applied to jazz).