One 512x512 atlas is certainly going to be better than 4x256x256. But that isn't what the atlas spanning feature is for - its for convenience when you have a lot of animated sprites, for instance. Think of a scenario where you have loads of sprites for an animation, which will take say 2x1024x1024 atlases. But its for one animation, so only one of these will be visible at a time (per animated sprite).
Its a bad idea to use this for background sprites, etc. as the order in the atlases isn't guaranteed, but for the situation described above, it works reasonably well. You can obviously do better if you know which frames could possibly be drawn with others, but if you want that kind of control, simply create multiple sprite collections manually.