Inside of BiomeProvider, there is a method: getBiomes(WorldInfo).
Why do you have to populate this, if the generator itself already returns the biomes at any given position? It seems to be used in org.bukkit.craftbukkit.generator.CustomWorldChunkManager#collectPossibleBiomes(), my best guess is that the vanilla generator uses this to know how to generate the biome map? Wouldn't that still be useless since you're not using the vanilla biome gen anyways?