Well I was able to figure out a solution by forcing an inverse ScaleX on the root bone that applies on update - changing the scale once on Awake or Start doesn't seem to stick after you call a new animation. I think our issue was the way we are calling our animations - regardless of the flip, we are still calling lean left/right on both the objects, so they were just responding to the direction we gave them.

Basically what it says in the subject line. It seems like using flipX, or even rotating or inverse scaling the transform of the game object with the skeleton animation does not affect the direction of our animation.

I've attached a gif to explain the problem, let me know if I need to give any more information!

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Any updates on this?