they may as well be turning humanoid waste into food

Yeah, they are. Waste matter is reclaimed as energy/supplies for food production

It would imply that transporter and replicator technology are, basically, the same thing. I agree. This is supported by replicators and transporters having a very similar special effect on the show.

they’d have to be violating the laws of thermodynamics to get more efficient energy production than matter-to-energy conversion. I don’t follow here. Why do they ‘have’ to be? They could very well be spending more energy but the increased amount is ‘trivial’ from their perspective. This would not violate Thermodynamics.

Ah I think I see the confusion. They are using antimatter for energy creation. Energy to matter for transport or replication is ‘paid’ for by the matter to energy destruction of the og material (whether it be the transported individual, waste matter collected from the crew, equivalent amounts of reactor fuel, or some combination of these) and the excess cost of thermodynamics is paid for by the matter-antimatter reactions in the reactor.

Is the efficiency miraculous? Yes, ofc. Is it breaking thermodynamics? No. It’s easy to see how they are paying for the excess costs with reactor fuel and that is without any hand-wavium of subspace or dilithium crystals being involved.