I tried setting the scale on the root bone but it doesn't seem to change anything. Here is the code I'm using with the C++ generic runtime.
float widthRatio = newRect.GetWidth() / m_skeletonData->getWidth();
float heightRatio = newRect.GetHeight() / m_skeletonData->getHeight();
float scale = min(widthRatio, heightRatio);
spine::BoneData* boneData = m_skeletonData->findBone("root");
boneData->setScaleX(scale);
boneData->setScaleY(scale);
The size of the bounding box is 100x100 and I'm using the Spineboy sample which has a width and height of 419x686 so the scale calculated is about 0.145.