Are you also packing the PNGs into a texture atlas? If so, are you packing using rectangles or polygons? Packing polygons can take significantly longer and is unnecessary if your PNGs are all rectangles. There are a number of texture packing settings that affect the speed.
Image and video export use OpenGL and run in a single threaded manner. That means it won't be able use all your CPU threads to speed up exporting, so it's not surprising that you don't see 100% CPU usage. I'm afraid there is just a lot of work that Spine needs to do. Depending on what you are exporting it can take some time.
