Preheat your oven to 425°F (220°C). On two large rimmed baking sheets, combine the diced zucchini, eggplant, and bell peppers. Drizzle with 4 tablespoons of the olive oil, ½ teaspoon of the kosher salt, and the black pepper. Toss well to coat evenly, then spread into a single layer. Roast for 25-30 minutes, tossing halfway through, until the vegetables are tender and caramelized at the edges.
While the vegetables roast, heat the remaining 2 tablespoons of olive oil in a large Dutch oven or heavy-bottomed pot over medium heat. Add the chopped onion and cook, stirring occasionally, until softened and translucent, about 6-8 minutes. Add the minced garlic and optional red pepper flakes, and cook for another minute until fragrant.
In a blender, combine the can of no-salt-added crushed tomatoes and the rinsed cannellini beans. Blend on high speed until completely smooth and creamy, about 60 seconds. Pour this purée into the Dutch oven with the sautéed onions and garlic.
Stir the tomato-bean sauce to combine. Add the bouquet garni, pressing it down to submerge it in the sauce. Bring the sauce to a gentle simmer, then reduce heat to low and let it cook gently while the vegetables finish roasting to allow the herbs to infuse the sauce.
Once the vegetables are roasted, carefully add them directly to the simmering sauce in the Dutch oven. Stir gently to combine all the components. Continue to simmer for 10 minutes for the flavors to meld together.
Remove the pot from the heat. Discard the bouquet garni. Stir in the fresh lemon juice and the remaining ¼ teaspoon of kosher salt. Finally, fold in the sliced fresh basil. Taste and adjust seasoning if necessary. Serve hot, garnished with a final drizzle of high-quality extra-virgin olive oil if desired.