I think the main problem is going to be that dilithium just can't be replicated. It's a magic rock with magical properties, and replicating it is going to require too much something or other. The ability to replicate dilithium from scratch would ruin too many Star Trek
If dilithium is transuranic, then perhaps the in-universe explanation is a result of some issues from replicating the nucleus, and perhaps the problem is in common with many or all transuranics, including latinum
(assuming latinum is transuranic, too).