We are sorry to hear that you are facing troubles! 15-20 minutes instead of 4 seconds sounds very strange indeed. Have you tried what happens when viewed in the Unity profiler? Perhaps memory grows over a certain ammount due to a leak, or similar (however, this still does not justify 20 minutes).
How are you loading and unloading the chunks you described above?
I know this might be hard, but could you try to strip the project down to only some problematic Spine parts and the loading logic that still shows the problem? You can send the Unity project as a zip file to contact@esotericsoftware.com.
Perhaps you could just create a simply test scene which loads and unloads the same chunk several times.
It would also be very interesting if the same setup causes the same problem with version 3.8 of Spine and the spine-unity runtime. Unfortunately this will only be feasible when the project is already condensed to a minimal scope, as above.