The Future of 3D Printing?

I was thinking about Star Trek today, and gold pressed latinum. I was wondering why anything was rare in a universe with replicators when it hit me... the replicators aren't magic. They can't make something from nothing. What they do is kind of the same as the transporter and they take stuff from one place and arrange it properly 3d printer style somewhere else.

Now I'm not saying there's a ton of liquid Earl Grey tea kept at the perfect temperature.... more that the "recipes" for everything tell the replicator how to arrange the basic elements into what you ask for. That being said, if you don't have latinum (or gold), you just can't get the replicator to make gold pressed latinum. 

This led to thinking about huge blocks of carbon in a storage bay somewhere and the slow creeping realization that since they can sort atoms, there's no such thing as waste. All the carbon and nitrogen and hydrogen and oxygen in the air, or left over on the plates, or in the washrooms, are easily converted into tomorrow's birthday cake.

One thing I am still confused on is dilithium crystals. If they get overworked they get cracked... but why can't they break down the cracked one and replicate an un-cracked one? For that matter, why do away teams need to be rushed to the medical bay? Why can't they just be fixed by using their beaming down patterns as the recipe to rebuild on the way up? Infections and brain damage might not be do-able due to complexity but a giant hole in the gut? easy peasy. They might lose memory of those hours away but that's a small price to pay for not bleeding to death.

What do you think?