This would get into the wibbly-wobbly philosophical realm of consciousness, except Soul Gems make the whole discussion redundant: The Soul Gem is the seat of consciousness for Magical Girls, and the body is non-continuous external hardware. As long as the gem is able to identify the body as 'my body', it'll connect with it. Niko's Molecular Reconstruction breaks down and rebuilds matter in a matter almost identical to the Alchemy in Full Metal Alchemist; as long as she has a reasonably accurate blueprint (which Umika's magic can provide, by reading the Soul Gem's memories), she can transmute something like, say, a pig carcass into a human body that's indistinguishable from 'the real thing'.