Prepare pasta according to package directions and drain.
While it cooks, melt butter over medium heat in a large saucepan. Whisk in flour, dried mustard, and salt until combined. Pour in milk and chicken broth, whisking vigorously to prevent lumps. Bring to a simmer, stirring frequently, and simmer until thickened (5-8 minutes).
Stir in squash and cream cheese until cream cheese is melted. Remove from heat and stir in pepper and cheddar cheese until melted. Add chives, if using, reserving a few to sprinkle on top.
Toss cheese sauce with noodles, sprinkle with reserved chives, and let rest 5 minutes before serving hot - the sauce will thicken further as it sits.
Notes
To make spaghetti squash puree: Drizzle whole spaghetti squash lightly with olive oil or spray with cooking spray. Pierce all over with a fork or sharp knife and roast on foil-lined baking sheet at 400 degrees for about 1 hour, until you can easily slide in a sharp knife. Let cool slightly before cutting off stem end and slicing whole squash lengthwise. Gently scoop on seeds with a spoon and discard. Shred remainder of squash with a fork and remove to blender or food processor. Blend with just enough milk or water to make a smooth puree - add up to about ¼ cup of liquid. Puree can be stored in the fridge for up to a week, or frozen for longer storage.
Recipe by Hidden Ponies at https://hiddenponies.com/2013/07/lighter-creamy-homemade-macaroni-cheese/