Heat oven to 425°F. Toss squash with oil and 1/4 teaspoon salt on a sheet pan and roast for 25 to 30 minutes, turning once, until very tender.
Meanwhile, cook macaroni in a large pot of boiling water until just tender, following the package time; drain well.
Blend warm squash, cottage cheese, the 1 1/2 cups milk, mustard, remaining salt and pepper until completely smooth. Pour into the empty pasta pot and warm over low heat for 3 to 4 minutes, stirring.
Remove from heat and stir in cheddar a handful at a time until melted. Fold in macaroni; keep the sauce loose rather than simmering it down.
Divide among six shallow containers, refrigerate within 2 hours and chill fully. Cover and freeze for up to 2 months for best texture.
Reheat one frozen portion in a microwave-safe bowl with its measured milk under a loose microwave-safe cover at 50 percent power for 3 minutes. Break apart and stir, then heat at full power in 30-second bursts, stirring between them, until the whole portion reaches 165°F, usually another 2 to 4 minutes.