Preheat the oven to 425 degrees F (220 degrees C). Place a baking sheet on the lower oven rack.
Slice heirloom tomatoes into 1/2-inch rounds. Remove seeds with your fingers. Place 6 slices on paper towels or a clean cloth and cover with more paper towels or another clean cloth. Arrange the remaining slices on a wire rack. Cut Roma tomatoes into 1/2-inch slices, remove seeds, and arrange them on the rack as well.
Line a deep-dish, 9-inch pie plate with dough. Place 2 layers of aluminum foil over the entire surface. Fill with pie weights or dried beans.
Bake pie crust on the preheated baking sheet on the bottom rack. Place tomatoes on a higher rack. Reduce temperature to 400 degrees F (200 degrees C). Bake until the bottom of the pie crust has lost its translucent raw look and the edges have just started to color, 12 to 15 minutes.
Carefully remove the foil and the weights. Cover the edges of the crust with foil to prevent them from burning. Poke the bottom of the pie crust with a fork to keep it from puffing up. Return the pie crust to the bottom rack and bake until the bottom starts to color, about 8 more minutes.
Remove pie crust and allow to cool. Continue baking the tomatoes until they are wilted, about 40 minutes total. Remove and allow to cool. Keep the oven on.
Place bacon in a large skillet and cook over medium-high heat, turning occasionally, until some of the fat has rendered, about 5 minutes. Add sliced leek. Cook until bacon is crisp and the leeks have softened and browned, about 5 more minutes. Drain bacon on paper towels and allow to cool.
Place bacon-leek mixture, Cheddar, Fontina, mayonnaise, basil, egg, and mustard in a bowl. Season with salt and pepper. Mix to combine.
Spread 1/3 mixture on the bottom of the pie crust. Arrange 1/2 of the roasted tomatoes on top, overlapping heirlooms with Roma tomatoes. Spread another 1/3 of the mixture over the tomatoes and arrange the remaining roasted tomatoes on top. Add the last 1/3 of the mixture and gently press the fresh tomato slices on top in a decorative pattern. Arrange foil around the edges of the pie crust to protect them from burning, taking care that the foil doesn’t touch the tomatoes.
Bake until browned and bubbly on top, about 40 minutes. Cool completely before serving.