https://paste.dimdev.org/gonihatupu.mccrash

Superflat worlds won't generate at all.

I was having a similar problem? If I go in to create a superflat world, click customize the kind of superflat I would like, and then click done, it has changed back to RTG. There is no way to get it to stay as superflat.

Until the next build is released, in rtg.cfg set B:rtgWorldTypeByDefault to false. This will prevent the world type selection reverting back to RTG when exiting the Customize World Screen after configuring another world type, such as FLAT.

java.lang.IllegalStateException: Not a JSON Object: 3
    at com.google.gson.JsonElement.getAsJsonObject(JsonElement.java:90)
    at rtg.api.world.gen.RTGChunkGenSettings$Serializer.deserialize(RTGChunkGenSettings.java:572)
    at rtg.api.world.gen.RTGChunkGenSettings$Serializer.deserialize(RTGChunkGenSettings.java:560)
    at com.google.gson.internal.bind.TreeTypeAdapter.read(TreeTypeAdapter.java:69)
    at rtg.api.world.gen.RTGChunkGenSettings$Factory.jsonToFactory(RTGChunkGenSettings.java:415)
    at rtg.api.world.RTGWorld.<init>(RTGWorld.java:60)
    at rtg.api.world.RTGWorld.getInstance(RTGWorld.java:79)
    at rtg.world.WorldTypeRTG.getBiomeProvider(WorldTypeRTG.java:51)
    ...

You are going to have to provide more info than that, because that stacktrace is clearly showing that the game is starting with the RTG world type (not superflat). This is the only scenerio in which WorldTypeRTG#getBiomeProvider would get called.
The JSON parse error is because an erroneous chunk generator setting string is being passed that is not valid JSON.

I can not reproduce this at all.