How to Make It
Preheat oven to 375°F with oven rack in middle position. Combine torn bread, 1/4 cup Parmigiano-Reggiano, garlic, nutritional yeast, and salt in bowl of a food processor. Pulse until fine breadcrumbs form, 3 to 4 times. While pulsing, drizzle in olive oil, and process until oil coats all of the crumbs (you should end up with about 1 cup breadcrumbs). Transfer crumbs to a rimmed baking sheet, and bake in preheated oven until golden brown, crisp, and toasted, about 7 minutes, stirring once halfway through. Remove from oven, transfer to a large plate, and set aside.
Increase oven temperature to 400°F; keep one oven rack in middle position, and place another rack in upper-middle position. Use a vegetable peeler to peel squash. Separate the neck from the round base. Cut the neck in half crosswise, then cut lengthwise into 1/2-inch-thick planks. Cut the round base in half, and use a spoon to scoop out and discard seeds. Turn squash halves cut sides down, and cut into 1/2-inch-thick half moons. Place squash slices in a large bowl, and add sage, olive oil, thyme, honey, and salt. Toss to combine. Transfer squash mixture to a rimmed baking sheet, and arrange in a single layer. Roast squash at 400°F until slightly tender, about 15 minutes. Let cool 5 minutes.
Meanwhile, stir together marinara and soy sauce in small bowl; layer half of squash in a 11- x 7-inch baking dish. Spead 1 cup marinara mixture evenly over squash, sprinkle evenly with 1 cup mozzarella and 1 cup fontina. Repeat layering with remaining squash, marinara mixture, mozzarella, and fontina. Sprinkle evenly with Parmigiano-Reggiano. Cover with heavy-duty aluminum foil, and bake at 400°F 1 hour. Uncover and bake until squash is tender and cheese is golden brown, 20 to 25 minutes. Sprinkle with breadcrumbs, and serve.