A few months ago I picked up work at JB Games making art for Grave Danger. I had never used Spine before or animated anything really since a few classes in After Effects about 10 years ago so was coming into everything pretty green.
One element that I needed to create a workaround for in Spine was how the Spine exporter script used Groups to signify "Skins". This meant essentially that I couldn't use layers while painting different sprites because to export you would have to flatten everything.
One possible workaround I considered was turning each sprite (asset) into a smart object. This would let me have as many layers as I wanted but still allow the Spine exporter to read the 'flat' layer correctly. The problem with this method is that when you are working on a character comprised out of 20 smart objects, your painting flow gets really broken up when you can't quickly jump around adding and tweaking all elements at once.
Below is my solution. It could be wrong, it could be unnecessary because I missed something - or because Spine has since gotten an update - however, It worked out really well for me here and in a few other odd pipelines for the project.
Hopefully, somebody will find it helpful!