Spoon flour into sauce pan. Add milk slowly, stirring with whisk. Heat and stir over medium heat until thickened. (About 3 min.) Stir in cheeses, onion, mustard, salt, chipotle and stir for about 2 min.
Sitr together macaroni, cheese sauce, and tomatoes. Spoon into casserole dish. Top with breadcrumbs and some parmesan cheese. Cook at 375 for 20 minutes.