On your first point: it doesn't really bear scrutiny but I just took it as a given to prove that he has some legal rights.
On your second point: Starfleet scientists are probably overwhelmed with all the mysterious artifacts, Borg technology, and dead aliens the Enterprise keeps sending back. When the topic of "duplicate human" came up, they put their hands over their ears and went, "LA LA LA!"
Not to mention that they're conducting witch-hunts for Changelings, Augments, and Dr. Bashir. Starfleet Security might have clamped a lid on this one immediately.
On your third point: As posted earlier, there are probably lots of weird Federation laws on the books. If there weren't before, they wrote some new ones after this.