Yes, in a cloud layer Final Position is different from Position in Terrain/Texture if the cloud layer has "move textures with terrain" enabled. This is by design. It doesn't work properly in cloud v2 but it does in cloud v3 and easy cloud. It sounded like you thought it wasn't working this way and gave an example where you thought you needed to use Final Position, but I tested your example with Position in Terrain/Texture and it works the way I described here. So I guess I misunderstood what you were saying.
In a cloud you can use Position in Terrain/Texture but you have to be aware that it's different from Final Position because it's meant to be different. It's meant to be relative to the cloud space, not world space (unless you uncheck "move textures with cloud", and then they are the same). This is useful because you can create layers like you did in your example and then you can move the cloud to any height and your layers will continue to work.