I was able to solve the issue by changing all of my copy transform constraints to just location and rotation constraints. It turns out the way Blender exports FBXs is in a very specific order. So the scale of the bone was being added by it’s parent’s scale. In the unparented skeleton this wasn’t happening due to the fact that it had no parent that was scaling. So taking out the scale part of the constraint removes the added scale to the bone in the FBX export.