Place a large Dutch oven or heavy-bottomed pot over medium heat and add 3 tablespoons of the olive oil. Once shimmering, add the onion, carrot, and celery. Sauté, stirring occasionally, until softened and the onion is translucent, approximately 8-10 minutes.
Add the minced garlic, crushed fennel seed, dried rosemary, and red pepper flakes. Stir constantly until highly fragrant, about 1-2 minutes. Add the tomato paste and cook, stirring, for another minute until it darkens slightly.
Pour in the diced tomatoes (with their juices), the low-sodium vegetable broth, and the water. Add the bay leaves, ½ teaspoon of sea salt, and a generous amount of black pepper. Stir to combine.
Increase the heat to medium-high and bring the soup to a boil. Once boiling, reduce the heat to maintain a steady, gentle simmer. Partially cover the pot, leaving a small gap for steam to escape, and cook for 15 minutes.
Stir in the chopped seasonal vegetables, whole-grain pasta, and rinsed cannellini beans. Continue to simmer, uncovered, for another 15-20 minutes, or until the pasta is cooked al dente and the vegetables are tender.
Remove the pot from the heat and discard the bay leaves. Stir in the finely chopped kale (it will wilt in the residual heat), the fresh lemon juice, and the final ½ tablespoon of olive oil. Taste and adjust seasoning with more black pepper if needed. Serve hot, garnished with grated cheese if desired.