This is a current limitation of SkeletonAnimator because of the missing exposed parts of the Mecanim system.
If you want to get rid of the problems in transitions, you need to key all the dopesheet items between the animations that need to transition between each other, and disable autoreset.
SkeletonAnimation doesn't suffer from these transition problems.
We're working on a system that simultaneously removes this requirement for SkeletonAnimator and makes skeletons usable in Unity 2017.1's Timeline/Playables system. But it's a bit complicated, so it may take a while.