Press pie crust pastry into a 9-inch pie pan; sprinkle with 1/2 cup Parmesan cheese. Dip tomato slices in flour, coating both sides. Arrange a layer of coated tomato slices atop the Parmesan cheese. Top with half the onion, half the basil, half the salt, and half the black pepper. Repeat layering with 1/2 cup Parmesan cheese and remaining tomatoes, onion, basil, salt, and black pepper, ending with 1/2 cup Parmesan cheese.
Stir mustard and mayonnaise together in a bowl. Spread over Parmesan cheese layer.
Bake in the preheated oven until cheese is melted and bubbling, about 25 minutes.
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