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To roast the veggies: Preheat the oven to 425 degrees Fahrenheit with racks in the middle and upper third of the oven. Line two large, rimmed baking sheets with parchment paper to prevent the vegetables from sticking.
Place the cauliflower florets on one pan. On the other pan, combine the bell peppers and onion. Drizzle half of the olive oil over one pan, and the other half over the other pan. Sprinkle the salt over the two pans. Gently toss until the vegetables on each pan are lightly coated in oil.
Arrange the vegetables in an even layer across each pan. Bake until the vegetables are tender and caramelized on the edges, about 30 to 35 minutes, tossing the veggies and swapping their rack positions halfway (lower rack to upper rack, and vice versa). Leave the oven on at 425, because we’re going to bake the dish at the same temperature. If you end up with any stray burnt onion pieces, discard them, and set the vegetables aside.
Meanwhile, bring a large pot of salted water to boil. Cook the pasta just until al dente, according to package directions (it will continue to cook while it bakes in the oven, so you want the pasta to still have a little bite to it). Drain and return the pasta to the pot.
Add 2 cups of the marinara, the chopped basil, and 1/2 cup of the mozzarella to the pasta. Gently stir to combine.
It’s assembly time! Spread 1 cup of additional marinara sauce inside a 9×13″ baker. Top with half of the pasta mixture, and gently spread it into an even layer. Evenly sprinkle the roasted cauliflower on top, then dollop 1 cup of the cottage cheese over the cauliflower (it doesn’t need to be spread into an even layer), followed by 1/2 cup of the mozzarella.
Top the mozzarella with the remaining pasta. Then sprinkle the roasted peppers and onion on top, dollop the remaining cup of ricotta on top, then dollop the remaining cup of marinara on that, then sprinkle the remaining cheese all over.
Place a clean, rimmed baking sheet on the lower oven rack to catch any drippings. Place the ziti, uncovered, on top of the baking sheet. Bake for 30 minutes, then transfer to the upper rack for 2 to 5 more minutes until the cheese is deeply golden, if desired.
Remove the baker from the oven and let it cool for 10 minutes before serving (trust me). Sprinkle freshly torn basil on top, slice with a sharp knife, and serve.