Preheat the oven to 375°F. Spray a 9” x 11” glass baking dish with olive oil spray and set aside.
Bring a large pot of salted water to a boil. Add cubed butternut squash and cook for 5-6 minutes, until fork-tender. Using a slotted spoon, transfer the squash to a blender.
In the same pot, add the whole wheat elbow pasta and cook according to package instructions. Drain and return to the pot.
Add ½ cup vegetable broth, onion powder, garlic powder, 1 teaspoon kosher salt, and a dash of black pepper to the blender with the squash. Blend until smooth and creamy.
In a small bowl, mix together the panko breadcrumbs, Parmesan cheese, ¼ teaspoon salt, and a pinch of pepper. Set aside.
Melt the butter in a medium saucepan over medium heat. Add the minced shallot and sauté for 2 minutes. Sprinkle the flour evenly over the shallots and cook for another minute.
Gradually whisk in the remaining 1 cup vegetable broth and skim milk. Bring the mixture to a boil, then reduce the heat to medium-low and cook for 5 minutes, whisking frequently.
Remove the saucepan from heat. Whisk in the shredded Gruyere, cheddar, and the pureed squash. Season with 1 ½ teaspoons salt and black pepper to taste.
Pour the cheese sauce over the pasta and stir gently to combine. Transfer the mixture to the prepared baking dish.
Sprinkle the breadcrumb mixture evenly over the top. Bake for 25 minutes.
Switch the oven to high broil and cook for an additional 2-3 minutes, or until the breadcrumbs are golden brown.
Garnish with chopped chives if desired. Serve warm and enjoy!
