Preheat your oven to 375°F and grease a 9x13 inch baking dish with cooking spray or butter.
Toss the cubed butternut squash with olive oil, salt, and pepper, then spread on a baking sheet and roast for 25 minutes until tender and lightly caramelized.
While the squash roasts, sauté the diced onion in a large skillet over medium heat for 5-6 minutes until softened, then add garlic and cook for another minute.
In a large bowl, combine the roasted squash, sautéed onion and garlic, 1 1/2 cups mozzarella cheese, Parmesan cheese, heavy cream, thyme, and sage, mixing gently until well combined.
Transfer the mixture to the prepared baking dish and spread evenly, then top with remaining 1/2 cup mozzarella cheese.
In a small bowl, mix the panko breadcrumbs with melted butter, then sprinkle evenly over the casserole and bake for 25-30 minutes until the top is golden brown and the casserole is bubbling around the edges.