Bake in the preheated oven until the liquid has been absorbed and the squash is tender, 45 to 50 minutes. Toss together the Gruyere cheese, Cheddar cheese, bread crumbs, thyme, and rosemary in a bowl until evenly combined. Remove the foil from the baking dish, and sprinkle the squash evenly with the cheese mixture. Sprinkle the Parmesan cheese on top. Return to the oven, and bake uncovered for 15 minutes more until the topping is lightly crunchy and brown.