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Preheat the oven to 375°F. Cook macaroni according to package directions until just tender. Drain very well.
Meanwhile, melt butter in medium saucepan over medium heat. Stir in flour; cook, stirring constantly, for 1 minute. Slowly stir in milk. Bring to a simmer and cook, stirring constantly, until mixture thickens. Stir in Cheddar cheese, goat cheese, mustard and salt; lower heat to medium low and stir until cheese is melted. Remove from the heat and stir in squash purée. Stir in egg. Pour cheese mixture over macaroni and stir until coated.
Line a 12-cup muffin pan with paper liners and spoon macaroni mixture into liners. Sprinkle tops with Parmesan and bake until lightly browned and crispy on top, about 25 minutes. Cool muffins in the pans for 10 minutes. Eat warm or room temperature, or remove from the pan, cool on a rack, and refrigerate for up to 3 days.