Are your stone variants (marble, basalt, limestone etc.) generated during ore generation or at a later point?
I'm trying to use these stone variants as FillerBlockType for my ores but it doesn't work.
I also tested it with vanilla stone variants (andesite, granite and diorite) and the stone variants of the mod Embellishcraft. All these variants are generated as ores and I can replace them.
I took a look at your code but I cannot figure it out.

The stones are generated on the UNDERGROUND_ORES layer.