According to blame, EM has some unregistered configuredfeatures

[BugmanBugman]

https://hatebin.com/clhalkiffk

[TelepathicGrunt]

Yep. This can be an issue for mod compatibility as under certain conditions, unregistered ConfiguredFeatures can basically prevent other mod's registered ConfiguredFeatures from spawning if in the same generation stage.

By that I mean, if mod A adds an unregistered CF to the ore generation stage and the biome's codec reaches it first, it will choke and basically nuke mob B's registered CFs afterwards. Here's a case where BetterCaves forgot to register their CF and caused several CFs from Oh The Biomes You'll Go to stop spawning in the world: YUNG-GANG/YUNGs-Better-Caves#75

Here's a more detailed explanation of why this happens in the biome's codec:

Specifically, when you call .withConfiguration on a Feature, you create a ConfiguredFeature. This is what should be registered to the WorldgenRegisties at mod init (you can do it in FMLCommonSetupEvent so you have your config ready too if it is needed).

Anyway here's an example from my mod RepurposedStructures of me registering all my ConfiguredFeatures.
https://github.com/TelepathicGrunt/RepurposedStructures/blob/584433a0745338802c84e9f498dc063c1f5505f8/src/main/java/com/telepathicgrunt/repurposedstructures/modinit/RSConfiguredStructures.java#L72-L74

[ex0planetary]

Yeah, figured this would be an issue similar to Fruitful. Once again I'm doing some dynamic ConfiguredRandomFeatureList replacement.

Seeing as it seemed like only vanilla biomes were affected by that code I could probably just hardcode it for vanilla biomes - the replacing of the vanilla feature seems to do the rest for modded biomes. I'll tackle it soon™.