Heat the oven to 425 degrees F. Toss the squash, onion wedges and unpeeled garlic with the olive oil and salt on a sheet pan. Roast for 25 to 30 minutes until the squash is soft and browned at the edges.
Meanwhile, cook the pasta in well-salted water for 1 minute less than the package says. Drain and set aside.
Squeeze the roasted garlic out of its skins. Blend the squash, onion, garlic, milk, Greek yogurt, smoked paprika, mustard powder, nutmeg, cayenne, salt and pepper until completely smooth.
Pour the sauce into the pasta pot over low heat and warm it for 2 minutes. Turn off the heat, then stir in the cheddar and parmesan until melted and glossy.
Fold in the pasta and spread it in a baking dish. Toss the sourdough crumbs with the melted butter and scatter them over the top.
Broil for 2 to 3 minutes until the crumbs are golden and crisp. Finish with chives and serve hot.