Preheat the oven to 400 F.
In a small saucepan, melt 2 tbsp of butter over low heat and add 1 tbsp of the garlic. Let it simmer until the garlic is fragrant but make sure the garlic doesn’t burn.
In a large mixing bowl, add the butternut squash, whole sage leaves, the garlic-butter mixture, salt to taste, and 1 tsp of pepper and mix well until the squash is well coated in the butter. Spread the squash in an even layer onto a sheet pan. Bake for 45 minutes.
While the squash is baking, cook the pasta according to the package instructions. Drain well.
Once the squash is done roasting, reduce the oven temperature to 375 F.
Heat the milk in medium sauce pan over medium-low heat but don’t let the milk boil. Melt 6 tbsp of butter in a large oven-safe skillet or cast-iron skillet. Add 2 tbsp of the garlic and the minced sage leaves and cook for about a minute or until the garlic is fragrant. Add the flour and cook over low heat, stirring continuously with a whisk. While whisking, add the hot milk little by little, making sure there are no lumps in the sauce. Once all the milk has been added, let the sauce come to a simmer and cook for about 5-10 minutes until it has slightly thickened. Add the cheddar and parmesan cheeses, salt to taste, and 1 tsp of pepper and mix well. Add the pasta to the sauce and stir well until the pasta is coated well with the sauce.
Melt the remaining 1 tbsp of butter and mix with the panko breadcrumbs. Top the pasta evenly with the breadcrumbs. Bake for 30-40 minutes, or until the sauce is bubbly and the top is browned.