Preheat the oven to 400 degrees F.
In a small bowl, stir 3 tablespoons olive oil, oregano, thyme, red pepper flakes, 1 teaspoon kosher salt and 1/2 teaspoon black pepper.
On one of the prepared sheet pans, arrange the tomatoes, onions and garlic cloves into a single layer without overlapping. Drizzle with the oil-seasoning mixture.
Roast the tomatoes, onions and garlic for 25-30 minutes, until the tomatoes are slightly wrinkled and the onions are browned at the edges.
On the other sheet pan, toss the bread with 1 tablespoon olive oil, 1/4 teaspoon kosher salt and 1/4 teaspoon black pepper. Spread into a single layer. Toast in the oven until lightly golden, about 10-12 minutes.
To puree the soup, transfer the tomatoes, onions and garlic to a blender and pour in the vegetable broth and the reserved tomato juice from the can. Blend until smooth and pour into a large pot. (You can use an immersion blender by putting all those ingredients into a large pot and pureeing them. The soup will turn out smoother if you puree it in a high-powered blender.)
Warm the soup to your desired temperature over medium heat on the stove.
Divide the soup into bowls. Add a swirl of pesto and top with croutons and Parmesan.