I installed the mod recently and everything looks great. So I changed a config to set the water at Y 10 and below to be 100% instead of 40% and now all of a sudden, I am getting this weird generation where sand blocks are randomly generating right above bedrock...

Removing the mod is the only way to fix the problem. So... What gives? Why is this happening?

I'm not sure. I think this is because I'm using the biome's filler block when replacing bedrock. Was this under a desert?

Nope. This happens EVERYWHERE and only when Flat-Bedrock is enabled.

What version is this? And are you using other worldgen mods?

1.1.2 for Forge 36.2.0 on Minecraft 1.16.5. I tested this with just the mod by itself and it still happens and only when flat bedrock is enabled.