You can disable nuggets for ingots by going to that ingot's module blacklist and specifying nugget or by disabling them globally. Even with the global blacklist and specifying it in the gems themselves, the gem nuggets won't go away.

Can I see the config file?

Edit: I didn't realize that adding blacklists to an item that already had the global blacklist served as a whitelist instead. I am an idiot.

I dont see how that makes you an idiot when it doesnt say anywhere that blacklisting in both makes the ore specific one a whitelist.

sorry for not having docs