I cobbled together a small plugin to show me the spawnlist for a specific block. When testing WitchHuts I can see that TC creates the structure, but treats it like a normal Swamp Biome instead of a special biome.

spawnlist in a Hut with Terraincontrol:

spawnlist on a vanilla map:

http://www.minecraftforum.net/topic/1538820-bounding-box-outline-mod/ has a few more infos regarding spawning behaviour.

My Bukkit plugin is available @https://github.com/jinks/MobInfo but it's quite bare-bones.

Thanks for the detailed and helpful report, I'll certainly look into it.

😦

I'll need to override this method to properly spawn witches. It's used to recreate the bounding boxes. This will mean that I need to bypass Bukkit in yet another place. However, I'll finally be able to fix the "eyes of ender not pointing to strongholds" bug.

We do have it, too!

Hi, we got exactly the same problem.

Me too, but I'll need to override CraftBukkit internals, which is not that easy.

@jinks Do you know if every structure is spawned without mobs or just the witch huts?

At the moment this affects witch huts and nether fortresses as far as I know. (Does TC do nether stuff?) Other structures that have bounding boxes are village houses and temples (jungle/desert) but those don't have "special" mobs, so they probably are ignorable.
I have read a few reports that witches did spawn in a desert temple when it was very close to a witch hut in a bordering biome, this may indicate that the bboxes have some common base. There are also bug reports, that witch huts don't spawn witches if they are generated in part over a river biome going through the swamp. I guess mojang hasn't worked out all the kinks on huts either :)