Pizza Casserole

Name: Pizza Casserole
Ingredients: 3 tablespoons olive oil, divided; 1 pound dried penne pasta; 8 ounces baby portobello or cremini mushrooms; 1 small shallot; 2 cloves garlic; 4 ounces thinly sliced pepperoni, divided; 8 ounces low-moisture mozzarella cheese, shredded (about 2 cups); 1 tablespoon Italian seasoning; 1 teaspoon red pepper flakes (optional); 1/2 teaspoon kosher salt, plus more as needed; 1/2 teaspoon freshly ground black pepper; 1 (about 24-ounce) jar marinara sauce