When tinkering around, I noticed that WorldCreator#generatorSettings does not seem to apply to a world.

 
Using the example in the docs:
https://hub.spigotmc.org/javadocs/spigot/org/bukkit/WorldCreator.html#generatorSettings(java.lang.String)

new WorldCreator("void").type(WorldType.FLAT)
        .generatorSettings("{\"structures\": {\"structures\": {\"village\": {\"salt\": 8015723, \"spacing\": 32, \"separation\": 8}}}, \"layers\": [{\"block\": \"stone\", \"height\": 1}, {\"block\": \"grass\", \"height\": 1}], \"biome\":\"plains\"}")
        .createWorld();

The world appears to just be a normal flat world (see picture) ... the default 4 layers (bedrock, dirt, dirt, grass) are applying, not the ones in the generator settings.

Including a simple tester plugin.
To replicate:

• Run server (the plugin will load the world on startup)
• TP to the world "/execute in minecraft:void run tp 1 10 1"
• Dig down and you shall see the 4 default layers.

I have not tested this on vanilla, as I have really no idea how to do this in vanilla.