When IE is on, mods like The Undergarden or Mystical World use tags for their configuredfeatures (typically the ore feature which takes a tag for blocks to replace), their configuredfeatures blows up upon being parsed and nukes all other features out of their biomes.

This was reported to me on TelepathicGrunt/Blame#31. Blame is my mod that will check for broken configuredfeatures and it found that when Mystical World or The Undergarden are on but not IE, the two mods work fine and everything parses and spawns fine. But once IE is on, their stuff gets broken due to tags dying somehow. Also of note: the mods does code based configuredfeatures.

Blame: https://www.curseforge.com/minecraft/mc-mods/blame
The Undergarden: https://www.curseforge.com/minecraft/mc-mods/the-undergarden
Mystical World: https://www.curseforge.com/minecraft/mc-mods/mystical-world

Image of The Undergarden missing everything when IE is on:

Logs
With IE on:
latest.log

With IE off:
latest.log

Hopefully this helps! Something with IE is making the tags be unable to be used for worldgen which is quite problematic