I've always been under the impression that you need matter, along with energy, to replicate stuff. With food and drink, that's easy - there's always a ready supply of organic materials to be recycled
But for non-organic items, you would have to have a ready store of the base stuff. Thus, mining is still a thing that needs to be done. And, it seems the process works in reverse, too - you put your dirty dishes back in the replicator, and they disappear as magically as they appeared.
Also, it seems the replicator can only create something to a certain level of complexity. The food is never quite right (it seems the complaint is a certain blandness, or sameness, which would make sense). If GPL is sufficiently complicated in internal structure for whatever reason, it would be impossible to get quite right with your typical replicator.
But really, only the first thing really need apply. If you need latinum and gold supplies for replication of GPL, if it could be done, it wouldn't lose its value - you needed it in the first place. Heck, maybe GPL is made by replication in the first place - the replicator does the work of making the alloy, perhaps. In "Little Green Men", Quark says gold is fine as a payment for his tech, so obviously replicators aren't alchemy.