Preheat oven to 350°.
Remove 1 teaspoon adobo sauce from can; set aside. Remove 2 chipotle chiles from can; finely chop to measure 1 tablespoon. Reserve remaining chiles and adobo sauce for another use.
Melt butter in a Dutch oven over medium-high heat. Add chopped chiles, onion, bell pepper, and garlic; cook 4 minutes or until onion is tender, stirring frequently. Sprinkle with flour; cook 30 seconds, stirring constantly. Reduce heat to medium; add tomatoes. Cook 3 minutes or until thickened. Add reserved 1 teaspoon adobo sauce, pasta, cheddar cheese, cottage cheese, milk, Parmesan, and egg; stir to combine. Spoon pasta mixture into a 2-quart baking dish coated with cooking spray; top with breadcrumbs. Bake at 350° for 30 minutes or until bubbly.