Hello, i know this thread has been inactive for a couple of months but i came to share my solution to the same problem the opener asked about (since i'm having the same issue).

I use the spine animations in unity without baking them, instead i use a SkeletonAnimator with the auto-generated Mecanim controller.

What i did was create manually a new Animator Controller that uses the animations from the Spine-created controller, so when i export new animations from the Spine project i just delete the Spine-created animator and create it again with right click on the SkeletonData file -> Spine -> Instantiate (Mecanim).
And then i just drag & drop the new animations from the spine-created controller (from the project view) into my manually created animator controller (which has all the transitions and logic between states).

So my character on scene has its animator component using the AnimatorController i created manually.

I hope this workaround helps somebody, it's the best solution i came up with.

Cheers