Using Skins as demonstrated in the latest example will make it compatible with animations.
What you need to do is key the swaps between Skin Placeholders if you want them to swap properly at runtime, then just map those placeholder names to appropriate attachments at runtime.
There's no need to create a new slot per item.
Each slot can have multiple images, even if only one can be enabled at a time. (You can't actually enable/disable a slot at runtime. You can only choose the attachment for it, which can be empty.)
Also possibly useful, depending on the type of deformation, is Linked Meshes, which can also be created at runtime. Linked Meshes are meshes that follow the shape and deformation of a master or "parent" mesh but can have different textures mapped to them.
We're still writing the documentation for the mix-and-match features and hope to include a sample skeleton project as well.
https://github.com/pharan/spine-unity-docs/blob/master/Mix-and-Match.md
It's a work in progress. But feedback on any points you want us to hit are welcome.