EDIT: Ok, i have tested every ore, there are quite a few bugged ones:
1. Ore is in config but not present ingame (Lemurite, Kalendrite, Ignatius)
2. Ore ignores any harvest level set in config, even defaults=> any version is harvest level 0, even granite versions (Cobalt, Shadowiron, Vyroxeres, Alduorite, Ceruclase, Midasium, Vulcanite, Sanguinite, Eximite, Meutoit)
3. Small ores work okay (config - 1), main ores are always level 0, even granite versions (Prometheum, Atlarus)
Using latest 5.09.11 if that matters. Strange thing is that some of GT versions of Metallurgy ores work okay, some not. Added this issue to your github
Adding some to list of bugged ore harvest levels:
no config option for harvest level of lignite coal at all,
cobaltite ore ignores config (0 when set to 10),
tungstate ore ignores config (0 when set to 9),
opal ore ignores config (0 when set to 10),
amethyst ignores config (0 when set to 11), small ore ok
https://github.com/Blood-Asp/GT5-Unofficial/issues/301