Skeletal animation relies on the fact that children inherit the behavior from the parent, allowing for effects like this one on the windmill blades rotating in perspective:
http://esotericsoftware.com/spine-examples-windmill#Windmill-Blades
Unfortunately if you scale your bones in setup this will always happen.
If the character is smaller but can use a separate copy of the skeleton, as I understand you're doing here, a better approach may be the one suggested here, where the skeleton is imported through a json at the new scale, all in one go, avoiding the scale issue:
https://esotericsoftware.com/forum/d/9151-fitting-new-high-res-assets-with-a-smaller-skeleton/3
(skipping the step where you resize the assets since they are already in a different size)
If instead you wanted to keep them in the same skeleton, then maybe the approach shown here may help:
VIDEO