Toss squash, sweet potatoes, and oil in a very large bowl. Add red pepper flakes and 2 tsp. salt and toss to combine. Arrange on baking sheet with thyme sprigs. Roast, tossing once halfway through, until squash is golden brown tender, about 1 hour.
Meanwhile, prepare cranberries according to recipe.
Transfer vegetables to a platter and drizzle with cranberry sauce. (Be sure to drizzle while sauce is still warm. Chill remaining cranberry sauce.) Serve remaining cranberry sauce with the vegetables.