The TLDR is that back in the '90s the dairy industry was going through some serious struggles and to ensure that the dairy market didn't collapse on itself, dairy farmers hired lobbyists to convince the government to buy more cheese. And by more cheese they did. 

The government bought so much cheese from dairy farmers that they created "cheese caves" to house all the excess cheese. And then they realized they had to sell the cheese, so they started providing pizza chains and other food providers with more cheese than they could sell. 

Which in turn, meant pizza chains had to innovate, leading to the stuffed crust pizza.