In a large, (5.25 quart or larger) heavy pot, heat the olive oil over medium-high heat. Add the onions and carrots to the pot and stir. Saute until onions are starting to become translucent and soft, about 3 minutes.
Add the sage, thyme, chili flakes, garlic, and tomato paste to the pot and stir. Once the tomato paste is evenly distributed and the garlic is fragrant, about 30 seconds, add the butternut squash, zucchini, and chickpeas. Stir to combine. Season the vegetables generously with salt and pepper.
Add the crushed tomatoes and vegetable stock to the pot. Cover the pot and bring it to a boil. Then, simmer the soup until the butternut squash pieces are tender, about 20-23 minutes. Add the pasta to the soup and continue simmering until pasta is tender and cooked through, about 10 minutes.
Add the chopped chard to the soup and place the lid on the pot. Let the soup simmer until the chard is wilted and bright green, about 2 minutes. Check the soup for seasoning. Serve the butternut minestrone hot with drizzles of olive oil, extra chili flakes, freshly ground black pepper, sprinkles of vegan “parmesan”, or fresh bread.