The Unification is there to actually FIX Bugs inside other Mods. If other Mods add to the OreDict but don't use OreDict themselves (what is idiotic behavior on their side), then the Config gives you the option to fix it yourself. And don't tell me you only want Unification on vanilla Stuff, that is ridiculous and would have no effects at all. Unification makes it so that you only have one type of Ingot/Gem per Material instead of a dozen different ones with totally identical functionality.
And GT Inventories unificate no matter what, that can and should never be turned off.
If there is an Issue with a specific Mod then telling Bloody that one specific Mod is being stupid, might help setting a default Target (what in turn will fix all the morphed gems in the next update), what is used for fixing MAAAAAAAANY retarded Mods already.