Heat the olive oil in a large nonstick skillet over medium-high heat. Add the onion, fennel and eggplant and cook, stirring occasionally, until tender, 10 to 12 minutes. Stir in the garlic, red pepper flakes, 1 teaspoon salt and a few grinds of pepper. Add 1/4 cup water and cook, stirring, until the water is absorbed, about 2 minutes.
Stir in the tomatoes and cook, stirring occasionally, until slightly softened, 3 to 5 minutes. Remove from the heat and stir in the olives and vinegar. Let cool about 20 minutes, stirring occasionally.
Meanwhile, preheat the oven to 400 degrees F. Using a small serrated knife, hollow out the bread loaf, leaving a 1/2-inch-thick shell. Slice the cut-out bread into pieces and arrange on a baking sheet; drizzle with olive oil and season with salt and pepper. Bake until slightly toasted, 5 to 8 minutes.
Stir the basil and cheese into the vegetable mixture; season with salt and pepper. Fill the loaf with the dip and top with more cheese. Drizzle with olive oil and serve with the toasted bread and crackers and/or crudites.