Preheat the oven to 375 degrees F. In a medium bowl, mix together the onions and bell peppers.
Lay out 6 flour tortillas on a work surface. Cover the tortillas with a layer of shredded Mexican cheese. Top each with a small handful of onions and bell peppers, a little more Mexican cheese, and then another flour tortilla.
Heat a griddle or large skillet over medium-high heat. Gently toast each side of the quesadillas until the cheese is melty.
Top 1 toasted quesadilla with 2 tablespoons pizza sauce, spreading to the edges. Top the pizza sauce with 1/3 cup mozzarella and 2 tablespoons Parmesan. Arrange a few pepperoni slices on top of the cheese.
Line a baking sheet with parchment paper and arrange the pizza-topped quesadilla on top. Add another quesadilla on top and repeat the pizza process. Repeat until all the quesadillas are stacked on top of each other with a pizza layer in between.
Unroll the pizza dough from the tubes. Drape one dough over half of the quesadilla stack. Drape the remaining dough over the other half of the stack, overlapping slightly.
Press the dough over the stack tightly, and make sure the two doughs are sealed together by crimping slightly. Cut off any excess dough.
On the top of the pizza, spread 1/4 cup pizza sauce and top with mozzarella and pepperoni.
Brush the sides of the dough with olive oil.
Bake until the crust is golden brown, 50 minutes to 1 hour. Allow to rest for 5 minutes. Slice and serve warm.