In a large pot or dutch oven, heat olive oil over medium-high.
Add squash, apples, and onion and sauté until beginning to brown and soften about 10 minutes. Add sage, thyme, and garlic and cook 1 minute; season with salt and pepper.
Stir in broth, bay leaf, and Parmesan rind. Bring soup to a boil, then reduce to a simmer over medium and cover, cook 25-30 minutes, or until vegetables are softened.
Remove soup from heat and discard bay leaf and Parmesan rind.
Purée soup using an immersion blender or in batches using a standard blender.
Return soup to pot over low heat, stir in vinegar and milk (is using); season with salt and pepper.
Top servings with sage, pepitas, and Parmesan cheese.