Preheat oven to 425°.
Combine 1/4 teaspoon salt, rosemary, and pepper. Place squash on a foil-lined baking sheet coated with cooking spray; sprinkle with salt mixture. Bake at 425° for 45 minutes or until tender and lightly browned. Increase oven temperature to 450°.
Cook the bacon in a large nonstick skillet over medium heat until crisp. Remove bacon from pan, reserving 1 1/2 teaspoons drippings in pan; crumble bacon. Increase heat to medium-high. Add shallots to pan; sauté 8 minutes or until tender. Combine squash mixture, bacon, and shallots; set aside.
Cook pasta according to the package directions, omitting salt and fat. Drain well.
Combine flour and 1/2 teaspoon salt in a Dutch oven over medium-high heat. Gradually add milk, stirring constantly with a whisk; bring to a boil. Cook 1 minute or until slightly thick, stirring constantly. Remove from heat. Add provolone, stirring until cheese melts. Add pasta to cheese mixture, tossing well to combine. Spoon pasta mixture into an 11 x 7-inch baking dish lightly coated with cooking spray; top with squash mixture. Sprinkle evenly with Parmesan cheese. Bake at 450° for 10 minutes or until cheese melts and begins to brown.