Using the settings for structures in the biome configs doesn't have any effects. Villages and mineshafts, even ocean monuments (ocean) will spawn all over the place, even if structures are disabled in those biomes.

If you set "SurfaceAndGroundControl: Mesa" mineshafts will spawn in two times in the same place. That will spawn in two minecarts in the same spot, with the same inventory.

I'm using TC build #162 on Spigot 1.10.2 version 9797151-301db84

EDIT: Seems like the structure settings for mineshafts do work, however they still spawn in two times if "SurfaceAndGroundControl" is set to "Mesa".

I've just found the issue. Well... more like a temporary solution. You have to disable the structures and villages from the WorldConfig settings instead of the Biome's settings. Set the villages to false etc. I know... this way you cannot have only particular biomes with villages, but its better without any than these bugged, tall, double, village spawns

I'm also getting villages on top of villages, as well as ocean monuments in places they shouldn't be (i.e. in a small river).