When you create a custom superflat map based on the Nether enviroment Nether Quartz does not generate with it, even if you use netherrack.
Example Customization Code:
2;7,89,57x87,88,4x87;8;stronghold,biome_1,village,decoration,dungeon,mineshaft,lava_lake
If you click "Overworld" in a custom superflat generally ore is still generated in the stone layers. This should also occur if the Nether is the selected biome and you use Netherrack as the base material much like stone in the overworld