If it helps, I think I know why it is clipping but I don't think I can fix it (the developer will need to)
The bounding box is starting at the tip of the head bone but the size of the bounding box appears to be calculated off the actual bounds of the mesh, so the bounding box is being moved down to start at the tip of the head bone.
You can confirm this by showing bones and you will see the bounding box is perfectly aligned with the head bone tip, not the top of the actual mesh (if that makes sense)