My problem is, that I don't know exactly why this is, or seems to be, true.

I think, that there are lots of overlay meshes. Take this image as example:



You can see at two locations, that this is not a unique mesh, which is merged together with the wooden ground:



You can see, that the green mesh is laid over the surrounding. Then, with alphablending, you achieve a nice blend with the environment.

The same goes for the big rock-walls, I think they "just" use regular multitexturing or so and throw in some decals, and thats it.