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Heat butter in a medium saucepan over medium heat until foamy. Sprinkle flour over and cook, whisking constantly, 1 minute. Gradually whisk in warm milk. Bring mixture to a boil, reduce heat, and simmer, whisking often, until béchamel is thickened and no longer feels grainy when rubbed between your fingers, 6 to 8 minutes. Remove from heat and add 2 cups Parmesan, whisking until cheese is melted and sauce is smooth. Remove from heat and set aside in a warm place.

Working over a bowl use the large holes of a box grater to grate the onion; set aside.

Heat ¼ cup oil in a large saucepan over medium-high. Cook pancetta (if using), stirring often, until golden brown and beginning to crisp, about 4 minutes. Add grated onion and all its juice, minced garlic, and red pepper flakes; season with salt and pepper. Cook, stirring often until onion is softened and just beginning to color, 6 to 8 minutes. Add tomato paste and cook, stirring, until slightly darkened, about 2 minutes.

Add crushed tomatoes to the saucepan. Bring sauce to a simmer and cook, stirring often, until slightly reduced and flavors have melded, 20–25 minutes. Stir in basil and season with salt and pepper.

Meanwhile, preheat the oven to 450 degrees F.

Toss zucchini, remaining ¼ cup olive oil, ½ teaspoon salt, ½ teaspoon pepper, and dried herbs de Provence. Spread the mixture out onto a baking sheet in as close to a single layer as possible. Roast until tender, about 15 minutes.

While the zucchini is roasting bring a large pot of salted water to a boil over high heat. Add the pasta and cook for about 6 minutes. Since you will be cooking the pasta a second time in the oven, you want to make sure the inside is still hard. Drain the pasta well and set aside.

Once the zucchini is out of the oven, lower the temperature to 350 degrees F.

Gently reheat the béchamel, using a splash of milk if necessary to get it moving in the pan then transfer to a large bowl; add partially cooked pasta, roasted zucchini, and grated mozzarella; toss to combine. Add all but 1 cup tomato sauce and gently fold mixture a few times, leaving streaks of béchamel.

Transfer pasta mixture to a 3‑quart shallow baking dish, dollop with remaining tomato sauce, and scatter remaining ½ cup Parmesan over pasta. Bake until mozzarella is melted and sauce is bubbling around the edges, 15–20 minutes.

Heat broiler. Broil until pasta and cheese are dark brown and crunchy in spots, about 4 minutes. Let pasta sit 5 minutes before serving.