CRUST: In a large bowl, combine flour and salt. Cut in shortening with a pastry blender or fork until it resembles coarse meal. Add ice cold water, 3 tablespoons parmesan cheese, oregano and thyme leaves, stir to combine. With floured hands, divide the dough in half and shape into 2 disks. Wrap one disk in plastic and refrigerate or freeze to use at a later date.
On a well floured surface, roll out the other disk into a 13-inch round. Fold the dough in half and then into a quarter and transfer to a 9 1/2-inch deep dish pie plate. Unfold and arrange to fit into the pie plate. Fold the overhang under itself and crimp the edges. Take a fork and pierce holes in the bottom of the crust. Refrigerate until firm, about 20 minutes. Meanwhile, preheat the oven to 350 degrees.
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 minutes more. Transfer to a rack to cool.
FILLING: Heat 1 tablespoon olive oil in a large skillet over medium heat. Add the sliced onions and cook, stirring, until golden, about 15 minutes. Let cool. Meanwhile, thinly slice the tomatoes and place in a colander, sprinkle with 1 teaspoon kosher salt, let drain, about 30 minutes. Increase the oven temperature to 375 degrees.
In a large bowl, combine the 3/4 cup parmesan, mozzarella, mayonnaise, breadcrumbs, 2 tablespoons each chives and parsley, thyme, 1/4 teaspoon each kosher salt and pepper, and the sautéed onions. Spread evenly in the crust. Arrange the tomatoes on top. Drizzle with the remaining 1 tablespoon olive oil and season with pepper. Bake until the tomatoes are browned, about 50 minutes.
Garnish the top with the remaining 1 tablespoon each chives and parsley.