Heirloom Tomato Pie

2 prepared 9-inch pie crusts, unbaked
¾ c. plus 3 Tbsp. shredded Parmesan cheese
2 Tbsp. extra-virgin olive oil
1 large onion, thinly sliced
2¼ lb. mixed heirloom tomatoes
Sea salt
¼ c. shredded mozzarella cheese
1 c. shredded Monterey Jack cheese
¼ c. mayonnaise
3 Tbsp. breadcrumbs
3 Tbsp. chopped fresh chives
3 Tbsp. minced fresh parsley
½ tsp. dried thyme
Freshly ground pepper

For the crust: Place one prepared crust, rolled out into a circle, on your work surface, top with the 3 tablespoons of freshly shredded Parmesan cheese, and place the second crust on top of the cheese; roll the crusts out together into a 13-inch round. Transfer the dough to a 9½-inch deep-dish pie plate. Fold the overhang under itself and crimp the edges; pierce the bottom of the crust all over with a fork and refrigerate until firm, about 20 minutes. Meanwhile, preheat the oven to 350°.
Line the crust with foil, then fill with dried beans. Bake until the edges are golden, about 20 minutes. Remove the foil and beans and continue baking until golden all over, 10 to 15 more minutes. Transfer to a rack to cool.
Make the filling: Heat 1 tablespoon olive oil in a large skillet over medium heat. Add the onion and cook, stirring, until they are caramelized, about 25 minutes. Let cool. Meanwhile, thinly slice the tomatoes; sprinkle with 1 teaspoon of sea salt in a colander. Let the tomatoes drain, gently turning occasionally, about 30 minutes. Place the tomatoes on a clean kitchen towel or paper towels to dry off some of the liquid.
Increase the oven temperature to 375°. Combine the remaining 3/4 cup Parmesan, the mozzarella, Monterey Jack, mayonnaise, breadcrumbs, 2 tablespoons each chives and parsley, the thyme, ¼ teaspoon each kosher salt and pepper, and the sautéed onion in a bowl; spread in the crust. Arrange the tomatoes on top of the cheese mixture and drizzle with the remaining 1 tablespoon olive oil and season with pepper. Cover the edges of the pie crust with foil or pie crust shields and bake until the tomatoes are browned, about 50 minutes. Top with the remaining 1 tablespoon each chives and parsley.