Currently when creating a custom biome and using custom blocks for any of the material layers. Caves will not generate through them.
The only way to get caves to generate is to generate a biome with stone and dirt, then have an ore feature that replaces large amounts of stone and dirt with the desired block run on the pre-underground phase of generation.
It works, but sometimes there's a few blocks that don't get replaced. Not to mention the more iterations you run (to make it more accurate) the more laggy it is to generate that biome.