The Defiant still carried an NX registry when it was destroyed. That conceivably makes the rules different for it.
If it was still considered an "experimental" testbed, the Starfleet rules might allow for the NX registry vessels to retain their original registries, since if the Defiant had blown up during shakedown (e.g., Sisko says the ship "nearly shook itself apart" when they first tried the design) it might allow for the registry to stay the same, unlike a class of ship that’s in full production.
I gotta guess they try out some ideas that blow up in their face at first before they figure out a practical version.