Preheat the oven to 425°F, line a baking sheet with parchment paper, and grease a 9x13-inch baking dish.

Slice the squash in half lengthwise and scoop out the seeds. Drizzle the cut sides with olive oil and sprinkle with salt and pepper. Place cut side down on the baking sheet. Place the shallots on a piece of foil, drizzle with olive oil and sprinkle with salt, and wrap tightly. Place on the baking sheet and roast for 30 to 45 minutes, or until the squash is soft.

Make the topping: In a small bowl, place the panko and olive oil. Toss to combine.

Bring a large pot of salted water to a boil. Prepare the pasta according to the package instructions, cooking until al dente. Reserve 1 1/2 cups of the starchy pasta water before draining.

Measure 2 cups of the cooked, soft squash flesh and transfer to a blender with the 1 1/2 cups pasta water, the shallots, olive oil, balsamic vinegar, salt, onion powder, garlic powder, sage, nutmeg, and several grinds of pepper. Blend until creamy.

Return the pasta pot to the stove and heat the almond milk over medium heat. Stir in the squash sauce and cook, stirring often, for 3 minutes, or until warmed through. Whisking constantly, gradually add the cheddar, Gruyere, and pecorino cheeses, making sure each addition is fully melted before adding the next. Whisk until all the cheese is fully melted and the sauce is creamy, then add the pasta and stir until coated.

Preheat the oven broiler and transfer the pasta to the prepared baking dish. Top with the panko and broil for 5 to 10 minutes, or until the topping is crisp and browned.

Let stand for 15 minutes before serving.