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.