Preheat oven to 400°F. Prepare two rimmed baking sheets with parchment paper and set aside.
Peel and cube butternut squash, sweet potatoes, and carrots into ½” pieces (about 6 cups of butternut squash, 4 cups of sweet potato, and 2 cups of carrots). Divide veggies between prepared baking sheets. Drizzle each pan with one tablespoon of olive oil.
In a small mixing bowl, combine two teaspoons of salt, cinnamon, chili powder, cumin, and black pepper. Stir to combine seasonings thoroughly, then sprinkle ⅓ of the seasoning blend over each pan of veggies, reserving last ⅓.
Toss to coat each pan of veggies evenly in oil and seasonings. Roast vegetables at 400°F for 15 minutes.
While vegetables roast, peel and cut onion into 8-10 wedges, about ½”-¾” wide (about 1 ½ cups of onion slices). Peel garlic cloves, then toss both with remaining ½ tablespoon of olive oil and ½ tsp. salt.
Carefully remove baking sheets from oven and add onion and garlic. Return to oven and roast for another 20 minutes.
When vegetables are almost done roasting, melt butter in a large pot over medium heat. Stir in remaining ⅓ of seasoning mix and cook for one minute.
Transfer all roasted veggies to the pot. Pour in broth, then bring pot to a boil. Turn down to a simmer and simmer for fifteen minutes. While the soup simmers, remove cottage cheese from refrigerator and let it come to room temperature.
Stir apple cider vinegar and chopped thyme into soup. Use an immersion blender to blend soup until smooth, or work in batches to carefully blend it in a blender.
Spoon cottage cheese into blender or a food processor. With blender running, slowly drizzle in about ½ cup hot soup to temper it, blending until very smooth and warm (add more soup if needed).
Stir warm blended cottage cheese into pot of soup. Taste and season with more salt or pepper. Serve hot with fresh herbs like parsley, chives, or more thyme.