Preheat oven to 400°.
Bring water to a boil in a large saucepan; add cauliflower and 1/2 teaspoon salt to boiling water, and cook 4 minutes or until tender. Remove cauliflower with a slotted spoon, reserving cooking liquid; set cauliflower aside. Bring cooking liquid to a rolling boil. Add pasta, and cook 7 minutes or until al dente; drain and set aside.
Lightly spoon flour into a dry measuring cup, and level with a knife. Combine flour and milk in a saucepan, stirring well with a whisk. Stir in thyme and garlic; cook over medium heat until thick (about 8 minutes), stirring constantly. Remove from heat; stir in 1/4 teaspoon salt, cheeses, onions, mustard, and pepper. Combine cauliflower, pasta, and cheese sauce in a large bowl. Spoon the cauliflower mixture into a 13 x 9-inch baking dish. Place bread in food processor; pulse 10 times or until coarse crumbs form to measure 1 cup. Combine breadcrumbs with butter; sprinkle evenly over cauliflower mixture. Bake at 400° for 20 minutes or until lightly browned.