The replicators use either energy to produce un complex molecular patterns or get the mass from it being stored in resivoirs or energy itself. It doesn't produce out of thin air.
They kind of did the same transporter trick, with Pulaski's affliction in Unnatural Selection. Definitely seems like they've stumbled onto some fountain of youth thing there The Tom Riker incident had just as much to do with the unusual nature of the distortion field from which his pattern was reflected as it did their technology. It's an entirely random anomaly, in conjunction with the use of a second transport beam, that created him somehow
From the way it's described in the episode, Will and Tom would be more like when a egg divides in the womb resulting in identical twins. Neither is a copy of the other, neither is a reproduction. They are both the original of the Riker who was being beamed up to the ship when the beam was split by the transporter operator.