So I've tried both approaches, using SkeletonAnimation and Mecanim. I have a simple test I'm trying to complete. I have a walk animation cycle with a character that blinks rapidly. I have a separate blink animation with a normal once every 2 seconds blink. I want to see the character walk and blink normally. I.e. perform an animation override when combining animations.
With Mecanim: I've set my base layer to loop my walk animation, my second layer to loop my blink animation with a weight of 1. Then on my SkeletonAnimator script, I set my two mix layers to : Always Mix, and then : Spine Style. Though it doesn't matter what I set these too, it always will add the two animations instead of overriding the eyes with the blink animation.
In the SkeletonAnimation approach, I wrote a simple script that would call skeletonAnimation.state.SetAnimation for my walk and blink, this way they should both be weighted to 1. I also made sure the animations were being played on separate tracks. I still end up with a mix of the two animations. Another interesting note, my root bone animation no longer works after setting the second animation.
As for specs, I'm running Unity 5.3.0f4 on a PC durring these tests. My target platform is set to android.
I'd love to know if anyone is able to get Animation overrides to work and how.