Okay, so here's how Mami's existence works, as far as I know:
Physically, her body is still human and still largely registers as human if a doctor's doing a physical exam.
Magically is where it gets dicey. She radiates magic, fairly normal on the train, but if he can sense placement of souls, he'd sense that her soul is contained inside the gem.
Kyubey explicitly calls the girls no longer human, so she wouldn't register as human but something else...undead.
sense stuff (madoka series spoilers)
Physically, her body is still human and still largely registers as human if a doctor's doing a physical exam.
Magically is where it gets dicey. She radiates magic, fairly normal on the train, but if he can sense placement of souls, he'd sense that her soul is contained inside the gem.
Kyubey explicitly calls the girls no longer human, so she wouldn't register as human but something else...undead.