I like Soban's idea
There should be huge energy tradeoffs with atomic/subatomic level fabrication, either through nanotechnology or through teleportation. You can do so in a pinch, but if the entire society was doing that every day they'd be speeding their way to the heat death of the universe.
I started thinking in a parallel way when working on that white paper I mentioned a while ago (which needs another draft). Basically Yamatai and her enemies can field troops in the trillions and ships in the millions. Effective use of those forces and better technologies make them more effective, but ultimately war on that scale would come down to how quickly you can produce units, and how much resources you have access to produce them. Yeah a KIA Neko can be brought back by an ST backup, but every vat being used to reconstruct someone is a vat not used on a new unit.
In my opinion this 23rd generation warfare would ultimately come down to how quickly you can generate energy, how quickly you can expend that energy and how efficiently that energy was used in expending the energy of the enemy.
That is to say, while Yamatai has the capability to print the elements they want out of pure energy, mining would be ultimately more energy efficient and not gone out of vogue.
But that's just my opinion from what I've seen of the setting so far, and my issues with the Star Trek Deep Lore. Roddenberry had some political goals with TNG, where the replicator made its debut, the actual mechanics of it are adhoc.