AFAIK, Texture Packer Pro does not use the polygons from the skeleton data when it packs. Because of that, I'm not sure its polygon packing can be used with the Spine Runtimes. If it can, that is great and you might as well continue using it. I believe Spine can pack polygons more tightly, but clearly Spine doesn't handle Square
as well.
Note that last I checked Texture Packer Pro did a poor job of automatically generating polygons
it can cut off non-transparent pixels, especially with low vertex counts.