1. Preheat oven to 375°.
2. Melt butter in a small saucepan over medium-high heat. Add pancetta; cook 1 minute. Add shallots and garlic; cook 2 minutes, stirring constantly. Weigh or lightly spoon 1.1 ounces (about 1/4 cup) flour into a dry measuring cup; level with a knife. Add to pan; cook 2 minutes, stirring constantly with a whisk. Stir in thyme. Gradually add milk, stirring constantly with a whisk; cook over medium heat until slightly thick (about 3 minutes), stirring constantly. Stir in Parmigiano-Reggiano; cook 3 minutes or until cheese melts. Stir in salt and peppers. Remove from heat.
3. Cook baking potato in boiling water 4 minutes or until almost tender; remove with a slotted spoon. Cook sweet potato in boiling water 4 minutes or until almost tender; remove with a slotted spoon. Cook butternut squash in boiling water 4 minutes or until almost tender; drain. Sprinkle vegetables evenly with remaining 1 tablespoon flour. Arrange potatoes and squash in alternating layers in a broiler-safe 11 x 7-inch baking dish coated with cooking spray; spoon sauce over potato mixture. Top with Gruyère. Bake at 375° for 40 minutes.
4. Preheat broiler. Broil 3 minutes or until golden. Let stand 10 minutes.