I've (roughly) drawn your root bone's axes, X in black, Y in green:
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When you set scaleX to -1, the root bone X axis will point in the opposite direction. This means everything is flipped over the Y (green line in the screenshot) axis.
Another way to say you want to make your character face left/right is that you want to flip it over the Y world axis. To do this you can leave the root bone rotation at 0 so the root bone X axis aligns with the X world axis, then scaleX -1 will do what you want.
Flipping the skeleton over a world axis and setting the root bone scaleX to -1 are almost the same thing, but they do differ slightly. If you have bones that don't inherit scale, flipping by setting scale X or Y to -1 will not flip those bones. At runtime the skeleton has a flipX/Y property which is like negative scale, but affects all bones, even those that don't inherit scale. We plan to expose this property in the editor.