Versions

Minecraft Version: 1.12.2
Silent's Gems Version: 2.6.9b
Silent Lib Version: 2.2.17
Modpack and Version (if applicable): N/A

The Issue

It seems the gem geodes are spawning in the sky in superflat worlds (and possibly other world types where the sky is in geode range?) They always have an air block in the center and one block on each side. The blocks are usually gems, sometimes hardened rock.

(edit) The same structures can also spawn in deep oceans.

Glad to see you already know about this. Cool mod, BTW. Love the enchantment tokens.

I just found a cluster of hardened netherrack with a couple of nether gem ores inside it in the overworld. Related to this?

Ah. OK.

The gem geodes are meant to spawn in the overworld. Gems in the center with a hardened rock netherrack/endstone shell.