1. Whether your character would 'feel' different to him than a baseline human: Ellie's fully human, buuuut the two smallest fingers on her left hand are cybernetic implants! They're made to look as natural as possible, and they move and have touch feedback for her nerves. He's free to pick up on that, and they're not anything special otherwise.
2. Whether your character has any ability to disrupt his power: Nope! However, if he can sense the signature of her fingers/implant he may still be able to sense her nearby even if she's using her power (invisibility).
3. Whether you would want to opt out of John sensing your character's field: Totally fine with this! I actually think it could be interesting to play with.