Well, I tend to accept unrealistic ideas in things like videogames, mostly because they don't need realism to be fun
But if you want to pretend we can explain it, however equally unrealistic this shall be, I would suggest that much in the way physical teleportation would separate an object into its individual molecules, the suit Samus wears would then compress her "free-floating" cells into the ball until the time to reform her. And she controls her movement with psychokinetic powers. Definitely. o_________o