The biggest difference is that ships like the Ent-D and Defiant could put into a Federation Starbase inbetween episodes. VOY did have that facility, as for replicating it. Sure thats a remote possibility but weren't there supposed to have resource issues. As for repairing it inbetween episodes. You've got to think that some would have to be running the ship at any one time, a few on sleep cycle so maybe at most you could call on a hundred crew members. Not all of which are engineers. Compared to a Spacedock or space station with reapir facilites that may be able to call on double that number or more to work on fixing a ship.
And the Defiant did have access to a spacedock, Deep Sapce Nine, during the Dominion war we did see scenes concerning reapiring battle damaged ships. So Starbase Deep Space Nine had the ability to serve as a reapir base.