In 8th edition, anytime a template hits a mounted monster, the template hits everyone on it. So, in the case of the stegadon it hits all the riders and the stegadon.
This counts for cannons aswell. So every model gets hit with the cannon ball. Also if its a stonethrower with a different strength under the center you have to randomise which model gets hit with the higher strength.
We knew about the rider and templates we just weren't sure if the template would hit one skink or all of them. Thanks for the clarification.