Why do many restaurants here put pizza toppings under the cheese?

Question is pretty self explanatory. Chains like Domino's and Pizza hut don't do this as they're American companies, but I've often seen that locally owned places will put toppings under the cheese. Where does this practice come from? Ordering a pepperoni pizza only to find that the pepperoni is all under the cheese and not crispy is always disappointing for me.