Being able to duplicate quartz, apatite, niter, and cinnabar obviously makes sense, but why have the result of growth be a pure crystal? Sure, it looks cool, but it can't be used for all the same recipes; only authentic, non-purified nether quartz can be used to make cobblestone into diorite, or diorite into granite, for example. I can't honestly think of a gameplay reason to have the pure crystals. If there's something I'm missing, that's all well and good, but if it's just there to differentiate it from before the seed-based duplication, why keep that differentiation in there if it's so much more work to add in all the recipes from before it was duplicated?

Pure crystals form beacause they are made using the spout and carefully precisely spouting liquid on them, that makes them grow in a controllable manner without any external inputs like in a natural environment. I will make all recipes that require the crystal input to be interchangeable with the pure version of them.