I know what you mean for frustration (I live in CO). But I think the reason why is that the FDA has “federal” jurisdiction. Marijuana is not legal on a federal level, it’s legal on a state level. Another example, let’s say that a company manufactures drugs, but as long as all their ingredients, distribution, etc. is within the state, the FDA doesn’t have jurisdiction (even though this situation is rare).
I don't know if the courts deal with this sort of question on an industry by industry basis, but for the most part, the fact that an activity is wholly intrastate does not preclude federal regulation. All activity affects interstate commerce, and that is the hook that courts use to uphold the regulations. A fellow by the name of Reynolds built a gun in his basement, never sold it or offered it for sale, and he was convicted of a federal firearms offense (California) under the rationale of Raich, which makes home-grown pot a federal offense.