When factored in at a per-figure cost, packaging is actually very minuscule. It doesn't really make a dent in the final price of the toy. If it was truly expensive, we would have been seeing more standardized shapes and fewer die-cuts and dimensionality.
It is once you factor in all the salaries of the art department and the approval process and the new planograms every time they change the package size, etc.. Indirect costs continue to add to this line..