Materia isn't what was farmed in FF7, it was a bi-product of leaks of the Life Stream hitting the surface. It had nothing to do with Shin-Ra, Make Reactors, or their impact on the environment. Reactors did cause them to be produced more often and Shin-Ra did develope a way to produce them on their own outside of Mako Fountains (Areas where Lifestream is rich in the soil and leaks upwards.) and reactors.
As for FFXIV. They can easily push lore that says the Aether that flows through the planet and allows Teleportation to work too and from Aetheryte Stones has a bi-product that allows crystals to form in rock, grass, trees, or underwater. And DOL have become adept slowly at locating and harvesting these stone for use by DOH to make Materia Crystals.
The fact is they can only call Crystals so many things. But they all mean the same thing in the lore of FF.
Crystal, Magicite, Materia, Have been the three most prominent.
Crystal is already in use. Magicite was used heavily in FFXI so they might want to mix it up for XIV which really leave Materia for this system as far as I see it.