Here's a scenario: You create your art at 5x resolution and design your skeleton and animations in Spine at this resolution. Now you want to use the art and skeletons in your game at multiple lower resolutions: 0.2 is normal size, 0.1 is half size for small screens, and 0.4 is double size for large screens.
You need three separate texture atlases at each of these sizes. The Spine packer doesn't currently do resizing, so you'll need to write a script with something like Imagemagick (freeware) or Photoshop to batch process your images to the needed sizes. You can then pack the images using Spine. Alternatively you can use Texture Packer Pro (3rd party payware) to pack the images (choose the libgdx texture atlas export format).
Now that you have 3 atlases, in your game you can choose the correct atlas and scale based on the user's screen size. For the 0.2 atlas set the SkeletonJson (SkeletonData in Unity) scale to 0.2, for the 0.1 atlas set the scale to 0.1, and for the 0.4 atlas set the scale to 0.4.
