Place pizza dough on a lightly floured work surface, and press into a rectangle. Spread a thin layer of marinara sauce on the dough to within 1/2 inch of the crust edges (you will not need all of the sauce), and top with mozzarella and Parmesan cheese. Evenly distribute pepperoni and onion over the cheese, and sprinkle with Italian seasoning, garlic powder, and red pepper flakes. Tightly roll up the dough to form a log, pinching the seam together to seal. Transfer dough to the refrigerator for 10 minutes to make slicing easier.

Preheat the oven to 425 degrees F (220 degrees C). Line a baking sheet with parchment paper. Using a serrated knife, slice the log into 12 individual rolls and set onto the prepared baking sheet. Bake in the preheated oven until pizza rolls are golden brown in color and the cheese has melted, 10 to 12 minutes. Serve pizza rolls with the remaining warmed marinara as a dipping sauce. Yields 12 pizza rolls.