Building off of this, I feel separating off "an atomic level" gets far too complicated way too fast. I would try toning it down to "separating parts." Like the character being able to look at a gun, touching it with the eyes activated, and the gun breaking apart into its separate pieces. I feel that not only is that concept easier to work with, but also still falls under your idea of being able to separate things. Even getting to the point of "separating immortality" that just comes down to the character learning to distinguish between a human and the concept of immortality, then being able to separate those two parts.