In large bowl, toss squash, carrots, onion, whole garlic cloves, chile, thyme, 2 tablespoons oil and ¾ teaspoon salt. Transfer to air-fryer basket and air-fry at 400°F, shaking basket occasionally, until vegetables are tender, 30 minutes. Discard thyme sprigs.
Meanwhile, in small skillet on medium, cook sliced garlic in remaining 2 tablespoons oil, stirring, until garlic begins to lightly brown around the edges, 2 minutes. Add pepitas and paprika and a pinch of salt and cook 1 minute; transfer to a bowl.
Transfer all but ½ cup squash to blender, add 1 cup water and puree, gradually adding 3 more cups water, pureeing until smooth. Reheat if necessary and serve topped with sour cream and spiced pepitas and with crusty bread if desired. Serve topped with remaining squash.
