It seems to me that scaleX and scaleY are swapped on the interface of Spine (and on the output files).
If you look at the transform interface, the translate box has a horizontal translate and a vertical translate (in that order), but the scale box has a vertical scale and a horizontal scale (in a swapped order), meaning that Spine considers a "scaleX" a scale along the Y axis.
I noticed this while using spine with my own drawing backend and then noticing I was doing scaleX/scaleY wrong (i.e., spine's worldScaleX was actually along the Y axis), then I went back to Spine and noticed it's also swapped on the interface.
Maybe I'm missing something?