Place the tomatoes in a large bowl. Put the parsley, basil, garlic, thyme, 1 teaspoon salt, and 1 teaspoon pepper in the bowl of a food processor fitted with the steel blade and process until finely minced. With the processor running, pour the olive oil down the feed tube and process until combined. Pour the mixture plus the lemon zest over the tomatoes and toss gently. Set aside.
On a well-floured board, roll the dough out to an 11 x 17-inch rectangle and transfer it to the prepared sheet pan. I used an 8 1/2" by 12" tart pan. Don't worry if it doesn't fit exactly; you want it to cover most of the bottom of the pan but it can be a little rough on the sides. Place a second sheet pan directly on the pastry and bake for 15 minutes. (You can also line the pastry with foil and fill it with dried beans.) Remove the top sheet pan (or the beans and foil). Using a dinner fork, pierce the pastry in many places. Bake for another 8 to 10 minutes, until lightly browned. Check the pastry during baking; pierce any spots that bubble up. Allow the crust to cool for 15 minutes.
Lower the oven to 375 degrees. Brush the mustard on the crust with a pastry brush. Sprinkle a thick even layer of Gruyere on the pastry, reserving 1/2 cup for the top, and sprinkle with the 1/2 cup of Parmesan. Place overlapping tomatoes in rows on top. If there is a little garlic and herb mixture in the bowl, sprinkle it over the tomatoes, but if there is liquid in the bowl, strain it through a very-fine-mesh strainer, discard the liquid, and sprinkle the garlic and herb mixture on the tomatoes. Sprinkle the reserved 1/2 cup of Gruyere and the remaining 2 tablespoons of Parmesan on top. Bake for 30 minutes.
Cool slightly, cut into squares, and serve warm or at room temperature.