In a large pot of salted boiling water, cook pasta according to package instructions. Reserve 1 cup pasta water. Drain and return pasta to pot. Meanwhile, in a medium saucepot, heat 1 tablespoon olive oil over medium. Add onion and half the garlic and saute. Add pepper flakes and bay leaf and cook until fragrant, 1 minute. Add tomato and juices, 3/4 cup pasta water, and salt and pepper. Bring to a rapid simmer and cook until tomato pieces begin to break down and liquid thickens, about 15 minutes. Discard bay leaf and, using a hand blender or food processor, blend tomato mixture until coarsely pureed. Toss with pasta to coat.
In a small skillet, heat remaining 2 tablespoons oil over medium. Add remaining garlic and cook until soft and fragrant, 1 minute. Add beans and remaining 1/4 cup pasta water and cook until beans are heated through. Stir in lemon zest and juice, and parsley. Season with salt and pepper. Divide pasta among bowls, top with warm bean mixture and sprinkle with Parmesan.