In a large Dutch oven, heat ¼ cup oil over medium heat until shimmering. Add eggplant and ½ teaspoon kosher salt and cook, stirring occasionally, until deeply browned and softened, 8 to 12 minutes. Transfer to a medium bowl and set aside. Wipe Dutch oven clean if remaining browned bits are starting to burn.
In now-empty Dutch oven, heat remaining ¼ cup oil over medium heat until shimmering. Add 1-inch zucchini pieces, onion, and ½ teaspoon salt and cook, stirring occasionally, until zucchini is browned and softened, about 6 minutes. Stir in garlic, thyme, and red pepper and cook, stirring constantly, until fragrant, about 30 seconds. Stir in reserved eggplant.
Add water, passata, and remaining 3 ½ teaspoons kosher salt to Dutch oven; bring to a simmer over medium-high heat. Add spaghetti, reduce heat to medium-low, and cook, covered, stirring often to prevent sticking, until spaghetti is just shy of al dente, 8 minutes.
Add ½-inch zucchini pieces and bell pepper to spaghetti and continue to cook, covered, over medium-low heat, stirring often, until pasta is al dente and vegetables are tender, 6 to 8 minutes more. Stir in fresh tomatoes and basil, remove from heat.
Divide evenly among 6 bowls, and garnish with olive oil, basil, and crushed red pepper.
