Preheat oven to 400°F.
Bring a large pot of generously salted water to a boil. Add butternut squash and cook until easily pierceable with a fork with no resistance. About 10 minutes.
Meanwhile, combine, panko, 2 tablespoons melted butter, thyme, and Parmesan cheese in a small bowl. Stir to mix and set aside.
Remove butternut squash with a slotted spoon and place in a blender. Add pasta to the same boiling water and cook al dente. Strain and set aside.
Add rosemary, milk, garlic, and 2 tablespoons melted butter to the blender. Blend until smooth and creamy. The consistency should be easily pourable and very creamy. If it's too thick, add more milk as needed. See note below on consistency.
Pour butternut squash into an oven-safe skillet or pan over medium heat. Season all over with salt and pepper, to taste. Add the cheese and stir until fully melted and creamy.
Add rigatoni and stir until fully incorporated. Top with panko mixture and bake for 10 minutes. For an extra golden crust, finish with a 1-2 minute broil. Top with additional thyme if desired.