Heat olive oil over medium heat in a large sauté pan. Add butternut squash and sauté until lightly browned, about 6-7 minutes.

Add red onion and sauté until tender, about 4 minutes. Add sausage, breaking it up into smaller chunks. Sauté until sausage is browned, about 3 minutes.

Add garlic, Swiss chard, and red chili flakes. Continue to cook until chard is wilted, another 3 minutes. Season with salt and pepper and keep warm.

While vegetables and sausage are cooking, bring a pot of salted water to a boil. Cook rigatoni until al dente, about 8 minutes. Drain pasta, reserving 1/4 cup of the pasta water.

Immediately add cooked rigatoni to the sausage mixture along with reserved pasta water, creme fraiche, and grated parmesan. Stir to coat pasta in the sauce and continue to cook for 1-2 minutes. Season with salt and pepper and sprinkle extra parmesan on top before serving.