These statements are problematic. Agito is mystical or it isn't. It's really not logical to say that Agito isn't mystical even though the thing that creates Agito is mystical.
If the Seed of Agito is mystical, then it makes sense to say the evolutions it causes are still a basically mystical process. For Agito to be truly "organic" like, say, Shin, I think there would need to be no magic involved in the process whatsoever.
(And yeah, I'm aware I'm arguing that, say, Amazon would be mystical by this argument. But why not? He's created by a mystic bracelet, how could he not be mystical?)