QuarryPlus and ChunkDestroyer can't dig buildings in Twilight Forest such as Lich Tower, Labyrinth and Dark Tower because of being not achieved the Advancements added by the mod.
The machines use fakeplayer, a dummy player for automation, which has Advancements just like normal players. The mod checks whether the players have completed advancements for the dungeon.

ChunkDestroyer doesn't dig "Highlands Center" because its block is too hard and require energy is more than 768000 RF (energy capacity of ChunkDestroyer).