In a large saucepan, cook pasta according to package directions. During the last 3 minutes of cooking, add broccoli and cook until tender. Reserve 1 cup of the pasta water, and then drain pasta and broccoli. Place in a large bowl.
Return pan to stove top, and combine milk and flour, stirring over medium heat until smooth. Cook until thickened (about 5 minutes). Remove from heat.
Add cheddar cheese, 2 tablespoon Parmesan cheese, cream cheese, mustard and crushed red pepper flakes to hot milk mixture and stir until cheese has melted and sauce is smooth. If needed, add reserved pasta water by the tablespoonful, to thin sauce to desired consistency. Add salt and pepper to taste.
Pour cheese sauce over pasta and broccoli, tossing to combine. Sprinkle with remaining Parmesan cheese.
Recipe by Alida's Kitchen at https://www.alidaskitchen.com/2013/08/08/cheesy-broccoli-penne-pasta/