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Combine butternut squash, shallots, garlic and oil on rimmed baking sheet, tossing to coat.
Roast in 425° F oven for 20 minutes or until squash is tender.
Transfer mixture to blender or food processor along with 1 cup water. Blend until smooth.
Place remaining 3 cups water and macaroni in large saucepan; bring to a gentle boil over medium heat, stirring frequently, so macaroni doesn't stick together. Once gently boiling, stir in evaporated milk. Bring back to a gentle boil; reduce heat to low. Cook, stirring frequently, for 10 minutes or until macaroni is tender and most, but not all, liquid is absorbed.
Stir in pureed butternut squash mixture, cheeses, mustard powder, salt and nutmeg. Heat through, adding additional water to thin if needed. Taste and season with additional salt and ground black pepper if desired.