As the current Metallurgy developer I should address the issue of Nether Quartz spawning in the overworld,
Metallurgy allows you to change the dimensions and spawn rates of vanilla ores via config files, Nether Quartz was originally set to dim 1 (the overworld) instead of -1 (the nether). After the next update this was fixed, however anyone who ran the old version still has configs telling it only to spawn in the overword. To fix the you must delete the Metallurgy Vanilla config file and let it regenerate
Metallurgy allows you to change the dimensions and spawn rates of vanilla ores via config files, Nether Quartz was originally set to dim 1 (the overworld) instead of -1 (the nether). After the next update this was fixed, however anyone who ran the old version still has configs telling it only to spawn in the overword. To fix the you must delete the Metallurgy Vanilla config file and let it regenerate