Just my two cents here, when I need to have multiple Spine skeletons interacting, but also need to animate each on their own, I simply keep all in one single Spine project.
Most of the time I only activate the skeleton I need to animate and forget about the rest.
When two skeletons have to interact in a single animation I activate just thw two and so on.
Since one can choose to export all the skeletons, just some, or just one, it's actually a very convenient workflow!
