Caves are not breaking the surface if the top/filler are changed.

This is odd -- the code in minecraft for digging blocks is that in most biomes, stone, top, or filler are valid for digging caves. I am specifically looking in a mesa, and the special-case biomes are beach, mushroom island, and desert.

Fixing this would require overhauling a portion of the generation code, something I'm not going to do with BiomeTweaker. I'm going to consider it as an unfortunate side effect.

Strange. I don't have time currently to play with it, but at first glance it should work fine. There are a few biomes for which topBlock and fillerBlock don't work, namely Hills, mutated Savannah, and special cases of Taiga. I'll look into this.

It's the mesas, more than anything -- the colored clay specifically.

Mesas have hard clay hard coded into their generation. If you change the top block, the cave generator derps out since it doesn't recognize the hard clay.

About a fix...err... I'll have to look into it more.

Ok. I'd like a way to select biomes by their class.

For now, I am just going to hardcode a few biome ID numbers. This is the special vanilla biome classes -- deserts (includes hills), mushroom (both kinds), and the mesas (already learned to leave them alone :-) ).

Hmm... Earlier I said that beaches are special-cased in vanilla code. But I'm actually not sure that that's right. Normally, vanilla will carve/dig through stone, filler, or top; but in these special biomes, it only digs in stone, dirt, and grass. I'm still not sure where/how the mesa caving operates, deserts and mushrooms ... hmm, mushrooms I can handle if I leave dirt, but on this map dirt is going to be valuable ... so, they just won't find caves in there. That's all.