One uses a system that can be fully understood by the user (Psionics)It still isn't a distinction that makes any sense to me. In all of the psionics threads no one has ever managed to even remotely coherently explain to me how one way of using the nature of the reality to levitate things with your mind is supernatural and other way of doing the exact same isn't.
One does not (Magic)
Basically D&D magic has parts a magic user will never understand and use logic that the magic user must accept but can't get why it worrks. Only deities and divine beings will get those parts.
Psionics has no such barrier. The user just has to be powerful enough and have enough knowledge or sense. Psionic powers make sense to the users and thats why they can modify it easily. Because its in their brain. It's like moving their limbs.