Arrange pepper halves in a 9-inch square glass baking dish. Cover the baking dish with plastic wrap and poke a few holes for vents. Cook in the microwave until tender, about 4 minutes. Set aside.

Mix together tomatoes with liquid, rice, and hot water in a medium microwave-safe bowl. Cover the bowl with plastic wrap. Cook in the microwave until rice is tender, about 4 minutes.

Remove plastic wrap carefully. Stir in kidney beans, corn, green onions, and red pepper flakes. Re-cover the bowl with plastic wrap. Cook in the microwave until heated through, about 3 minutes.

Spoon hot tomato mixture evenly into pepper halves. Cover the baking dish with plastic wrap and poke holes for vents. Cook in the microwave for 4 minutes.

Remove plastic wrap. Sprinkle stuffed peppers with mozzarella and Parmesan cheese. Allow to stand until cheese is melted, 1 to 2 minutes.