Heat oven to 425°F. Toss squash with oil and 1/4 teaspoon salt on a sheet pan. Roast 25 to 30 minutes, turning once, until very tender.
Meanwhile, boil macaroni in a large pot according to package time until just tender; drain well.
Blend warm squash, cottage cheese, 1 1/2 cups milk, mustard, remaining salt, and pepper completely smooth. Pour into empty pasta pot; warm over low 3 to 4 minutes, stirring.
Remove from heat; stir in cheddar by handfuls until melted. Fold in macaroni; keep sauce loose without reducing.
Divide among six shallow containers; refrigerate within 2 hours and chill fully. Cover; freeze up to 2 months for best texture.
Put one frozen portion and measured reheating milk in a microwave-safe bowl under a loose microwave-safe cover. Microwave at 50 percent power 3 minutes. Break apart and stir; heat at full power in 30-second bursts, stirring between, until all reaches 165°F, usually 2 to 4 minutes more.