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Preheat oven to 400u00b0F. Combine butternut squash, mushrooms, pepper, 1/2 teaspoon of
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the salt, and 1 tablespoon of the olive oil in a large bowl; toss to coat. Transfer squash
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mixture to a rimmed baking sheet. Spread in an even layer, and bake in preheated oven
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until tender, about 20 minutes.
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Heat remaining 1 tablespoon oil in a skillet over medium-high. Add onion, and cook,
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stirring occasionally, until caramelized, 25 to 30 minutes. Transfer to a plate.
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Combine milk, garlic, thyme sprigs, and oregano sprig in a medium saucepan over
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medium-high; bring to a boil. Remove from heat; cover, and let stand 30 minutes. Use a
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slotted spoon to remove herbs from milk; discard herbs.
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Add sausage to skillet over medium-high; cook, stirring often, until browned, 8 to 10
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minutes. Transfer sausage to a bowl lined with a paper towel.
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Melt butter in a medium saucepan over medium-high. Whisk in flour, whisking
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constantly, until there are no lumps. Gradually whisk milk into butter mixture; cook, whisking often until mixture thickens, 5 to 7 minutes. Whisk in Parmesan cheese, nutmeg, and remaining 1 teaspoon salt until smooth, about 20 seconds.
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Combine squash mixture, onions, sausage, and zucchini noodles in a large bowl. Pour
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butter mixture over squash mixture; toss to coat. Transfer to a buttered 9- x 13-inch
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baking dish. Sprinkle evenly with mozzarella, and bake in 400u00b0F oven until golden and
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bubbly, 30 to 40 minutes. Sprinkle with fresh thyme leaves.
