The problem relies in the fact that the rotation of the game is done only on the Z-axis.
When the skeleton is flipped, a rotation should be applied around the Y-axis too, to avoid the gameObject/collider to be upside down, I guess...
Oh, and by the way, thank you very much for your big involvement in the development of the Spine runtimes on the Unity/TK2D side and your activity on the forum. You're always a big help for Spine/unity users.😉