Preheat the oven to 350 degrees F (175 degrees C).
Heat oil in a skillet over medium heat. Add Roma tomatoes, chile sauce, corn, yellow bell pepper, green bell pepper, white onion, red onion, jalapeno pepper, and cumin. Cook and stir until tender, 5 to 7 minutes. Add refried beans and pinto beans; stir to combine. Remove bean mixture from heat.
Mix 1 cup Cheddar cheese, cottage cheese, and sour cream together in a bowl.
Cover the bottom of a 9x13-inch casserole dish with 1/3 of the bean mixture. Top with a third of the cheese mixture and a thin layer of tortillas. Repeat with another third of the beans, another third of the cheese mixture, and tortillas. Repeat again with remaining beans, remaining cheese mixture, and a final layer of tortillas. Sprinkle remaining 1/2 cup shredded Cheddar cheese on top. Cover with aluminum foil.
Bake in the preheated oven for 20 minutes. Remove aluminum foil and bake until bubbling, 8 to 10 minutes more.
Remove from oven and let stand for 10 minutes before serving.