i have made a custom biome, and i have selected:
VillageType: disabled
RareBuildingType: disabled
However, i have found swampHuts and villages spawned inside. (Version 2.8.2 snapshot)
https://s13.postimg.io/8c702dmjp/random_shit.jpg

also see: (1 more pic)
http://forum.mctcp.com/t/structures-in-biome-config-file-dont-work/1136

UPDATE
It seems that the world config overwrites the biome's structure settings (although it shouldnt)
If you want to disable those buggy villages etc, you have to set Villages to false from the WORLDCONFIG settings. I guess you cannot enable villages for particular biomes only... (with worldconfig villages to true and biome config to disabled or enabled)

This should be fixed now.