Preheat the oven to 425°F.
Line a baking sheet with parchment paper and lightly grease a 9x13-inch baking dish.
Halve the butternut squash lengthwise, removing the seeds.
Drizzle the cut sides with olive oil, season with salt and pepper, and place them cut side down on the baking sheet.
Wrap the shallots in foil after drizzling them with olive oil and a pinch of salt.
Place them alongside the squash on the baking sheet.
Roast for 30 to 45 minutes, or until the squash is tender.
In a small bowl, toss panko breadcrumbs with a bit of olive oil until well coated.
In a large pot of salted water, cook the pasta according to the package instructions until al dente.
Before draining, save 1½ cups of the starchy pasta water.
Once the squash is done, measure 2 cups of the soft flesh and add it to a blender along with the reserved pasta water, roasted shallots, olive oil, balsamic vinegar, salt, onion powder, garlic powder, sage, nutmeg, and pepper. Blend until smooth and creamy.
Heat the almond milk in the pasta pot over medium heat.
Stir in the blended squash mixture, cooking for 3 minutes until warmed through.
Gradually add the shredded cheddar, Gruyere, and pecorino cheeses, whisking continuously.
Let each cheese melt fully before adding the next.
Mix the cooked pasta into the sauce, ensuring it’s well coated.
Transfer the mixture into the prepared baking dish, sprinkle with the panko topping, and let the dish sit for 15 minutes before serving.
Boil for 5 to 10 minutes, or until golden brown and crispy.