Tom Riker was the result of a freak interaction between the ttansporter's confinement beam and the planet's unique force field. Presumably, doubling the confinement beam is an unusual procedure. In this case, the transport subject, Will Riker, made it through with just one of the beams. The other was "discarded" by the transporter operator. I assume that normally a discarded confinement beam just dissipates. This time, though, it interacted with the planet's doohickey field, and directly caused the materialization of Tom Riker. That's why I think Tom could be considered the duplicate, while Will is the "original". The subject that makes it through a normal transport cycle is considered the same person in Trek. Tom did not make it through a normal transport cycle, and it wasn't a failed transport, either. Since both Rikers had the same mass, one of them had to get his mass from somewhere else. I assume the transporter's interaction with the planet's doohickey field caused the energy of the field to be converted to mass, which materialized as Tom Riker. Will Riker's original mass made it through to the ship. Hence, Tom is a duplicate, while Will is not.
I can see that. Then he might have either a "confinement duplicate" tag assigned by the transporter to keep things straight, or his mass might read unusually to sensors due to its source. In either case they could legally prove he's a duplicate. What happens then (legally) is anyone's guess. But apparently duplicated humans are authorized to hold rank in Starfleet, or they wouldn't have returned him to duty. So duplicates have at least as many rights as Data has.
I'm still surprised that Tom was just shipped off to another posting like it was no big deal. Even if he wasn't a transporter duplicate, the fact that he'd been stranded alone for eight years should have earned him some medical leave. Surely he can't be considered fit for duty! Then there's the lab specimen aspect of his existence. You'd think transporter experts would want to study his accident, and medical doctors would want to examine him more closely - is he really a perfect duplicate? And what about the paperwork side? Is he issued a new, separate birth certificate? What's Tom's date of birth, anyway? Is it the same as Will's, or is it the date of the accident? Is Tom entitled to half of Will's estate, whatever that may be?
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.