Instantiation at runtime shouldn't affect batching. I do it all the time.
Can't imagine what else would be causing batching to break. The help article mentions the use of multi-pass shaders and stuff, if that applies to you at all. If you're just using the Skeleton shader that comes with Spine, it shouldn't be a problem.
Strange that I haven't come across this batching issue while using Spine's system.
... are you using just one material asset for the skeletons you intend to batch?