Heat oil in a large soup pot or Dutch oven over medium. Once hot, add onions and celery; cook 8 minutes, until soft.
Stir in garlic, chili flakes, butternut squash, and thyme sprigs; cook 4 to 5 minutes, until aromatic.
Add white beans, kale, broth, water, smoked paprika, salt, and pepper; increase heat to bring soup to a boil. Reduce heat to medium-low and simmer, uncovered, for 25 minutes, or until squash is tender.
Remove thyme sprigs, and stir in heavy cream, Parmesan, and sage. Taste and adjust seasonings as needed. Ladle soup into bowls and garnish with toasted pumpkin seeds and additional Parmesan cheese, if desired.