Using template attachments that you replace at runtime is a good approach, described here:
https://esotericsoftware.com/spine-runtime-skins#Creating-attachments
However, with 1x1 template images how do you control the position of the replacement image? The location of the center of the 1x1 image and replacement image will match, but you may need to create quite a large replacement image to get it in the right place. It would be mostly blank space and texture packing can trim off the blank space, but there may be a better solution.
More commonly the template image is large enough to contain any art for the slot. All replacement images are the same size, so you more easily know the position on the skeleton the art will appear.
I think your actual question is about how to use template with meshes. Create the mesh in Spine using a template image. At runtime, duplicate the template mesh and change the texture. The replacement image should be the same size as the template image.
A common approach for an avatar system is to configure the avatar with game items (clothing, armor, weapons, etc). Find the corresponding slots and template attachment, duplicate them, and replace the images so they look like the game items. Once you have the skeleton outfitted with all the correct images, you collect only those images and pack them into an atlas at runtime.
