The iridium, graphite and enderium essence seem to do nothing and some don't even appear in the JEI menu. Not sure if these seeds are disabled or broken. Currently have so much essence from these seeds that I can't seem to do anything with.

Yeah, they disable the essence

Is there a way to enable them in config as the owner?

The files for that are in the kubejs folder >server_scripts>mods>mysticalagriculture.