Preheat the oven to 400 degrees F. Bring a large pot of salted water to a boil and cook the penne pasta until just al dente. Drain and set aside.
Toss the butternut squash cubes with 1 tablespoon olive oil, 1/2 teaspoon salt, and 1/4 teaspoon black pepper. Spread on a baking sheet and roast for 20 minutes until tender.
While the squash roasts, heat the remaining tablespoon of olive oil in a large skillet over medium heat. Add the sausage and cook, breaking it up with a spoon, until browned. Add the onion and cook for 4 minutes until softened.
Stir in the garlic and cook for 1 minute. Add the chopped kale and remaining salt and pepper. Cook for 3 minutes until the kale wilts.
In a large bowl, combine the cooked pasta, roasted squash, and sausage-kale mixture. Stir gently to mix.
Transfer everything to a 9x13 baking dish. Sprinkle the mozzarella and Parmesan evenly over the top.
Bake for 15 minutes until the cheese is melted and lightly golden. Let rest for 5 minutes before serving.