Correct me if I'm wrong, but I think once we hit Next Generation time, replicators had evolved into a pure energy scenario.
Energy is converted into matter, which creates the specific atom you are looking for, and then repeated trillions of times to generate a specific pattern. We have technically done this with quarks (and why we believe they are the true indivisible particle of matter). In trying to break quarks, the amount of energy used actually created a quark. So theoretically it is possible to generate matter from an energy stream.
Ultimately that's a major major MAJOR step forward from just pure matter recycling, and so I think the recycling-based model is much more likely.