The default config will replace parts of all ore deposits with the default resources, that includes all modded ores. This is my "basic support" for all mods that add ores, I think it should work pretty well for most. The user made config should work with most mods that just add ores. You can replace ores from mods and use the modded ores as replacements.
If you have any specific idea for how to handle a mod, you can suggest it here and I might put it into an upcoming version. I kinda like the simplicity of the default config for now, but I might extend the rules for a couple mods. I mostly just dont actually know how to balance these small time mods, because I havent played with any. I've edited some of this back into the description of the mod.