In a 3-quart, enamel-coated Dutch oven or large nonreactive pot, heat the oil over medium heat. Add the garlic, shallot and salt. Stir to combine, then cook until the shallot is softened and translucent, 6 to 8 minutes. Add the crushed red pepper flakes, bay leaf and 1/4 teaspoon black pepper. Toast until fragrant, 1 to 2 minutes. Add the tomatoes, basil, tomato paste and Parmesan rind. Stir to coat with the oil and increase the heat to medium-high. Partially cover the pot to reduce splattering and cook, stirring occasionally, until the liquid has evaporated and the tomato mixture is thick, about 30 minutes. Add the vegetable broth and sugar. Stir to fully incorporate. Bring to a boil, then reduce to a simmer. Cover the pot and simmer for 10 minutes to marry the flavors. Turn off the heat and remove the lid. Cool slightly and remove the Parmesan rind and bay leaf.
Using an immersion blender, or transfer to a high-speed blender, puree the soup until smooth. Add the lemon zest and stir. Season to taste with salt as needed and add the remaining 1/2 teaspoon black pepper.
Ladle the soup into serving bowls. Drizzle with olive oil and a crack of black pepper. Serve hot.
When blending hot liquid, first let it cool for five minutes or so, then transfer it to a blender, filling only halfway. Put the lid on, leaving one corner open. Cover the lid with a kitchen towel to catch splatters, and pulse until smooth.