I noticed that using the infernal furnace from thaumcraft you still obtain thaumcraft nuggets, despite recalling seeing the fix in the scripts. Looking at the scripts i think all that is missing is mods.thaumcraft.SmeltingBonus.removeSmeltingBonus instead of only removeSmeltingBonus. So that should be an easy fix.

I just noticed, that was on 1.76a. But i checked the files on github that should be recent and they still have the same error, so it should be the same in recent versions.

Actually the scripts import mods.thaumcraft.SmeltingBonus.removeSmeltingBonus, so using removeSmeltingBonus by itself is fine.

Fact is, it doesn't work either way. Infernal furnace does spit out TC nuggets when processing native clusters. Didn't try with normal ores.

Worth a shot then, fingers crossed!

Pretty sure I found the issue, apparently the clusters have their own oredict, which is probably what the recipe is using.