That looks like an error.
Did you click Apply after setting up the dicing? Select all the field ones and make sure every single one of them is diced.
Also, please make sure you've not added the ones from the 2x directory, you're supposed to use the ones from the Textures directory, not 2x. 2x will need a larger atlas for hd sprites. You should be able to fit the atlas into a 2048 even with the sky images selected.
Yes, its packing like texture packer, but this tutorial does one thing texture packer can't do (as far as I know) which is dicing, it'll be obvious what it does once you've successfully built the atlas and look at the atlas texture - it massively reduces atlas size when used on larger images.