Rainbow Vegetable Gratin

Name: Rainbow Vegetable Gratin
Ingredients: 1 tablespoon olive oil, for greasing; 1 cup panko; 3 ounces Parmigiano-Reggiano cheese, grated (about 3/4 cup); 2 tablespoons chopped fresh thyme; 2 ½ teaspoons kosher salt, divided; ½ teaspoon plus 5 pinches black pepper, divided; 1 large red onion; 2 medium-size Yukon gold potatoes, unpeeled, sliced crosswise into 1/8-inch-thick slices (about 2 cups); 1 medium-size purple or orange sweet potato, peeled and sliced crosswise into 1/8-inch-thick slices (about 2 cups); 1 large zucchini, sliced crosswise into 1/8-inch-thick rounds (about 2 1/2 cups); 1 large yellow squash, sliced crosswise into 1/8-inch-thick rounds (about 2 1/2 cups); 2 large heirloom tomatoes (about 1 1/2 pounds), sliced crosswise into 1/4-inch-thick slices (about 3 cups)