What you describe is called "back painting", where you cut an image into layers, then paint each layer underneath the overlapping parts, so the layers can move in Spine and you'll see what you painted.
So far Spine doesn't edit your images, the idea being that you use Photoshop or other professional tools that do a better job. I do agree there are some advantages to editing tools being in Spine, or aware of Spine if they are 3rd party tools. You can see how that can work here:
https://www.linkedin.com/posts/leonardocunha_spine2d-gamedev-ugcPost-7447951254443409408-MoXq
We haven't decided if we want to go down that route. It is nice for us to focus on giving you new things you can do in Spine, without being distracted by the very large project that is helping you edit images for Spine.
