Cook bacon in a 4-to 6-quart heavy pot over medium heat until crisp. Transfer bacon to paper towels to drain. Add garlic and caraway seeds to fat in pot and cook, stirring occasionally, until garlic is pale golden, about 1 minute. Add squash, carrots, apple, thyme, bay leaves, broth, water, 3/4 teaspoon salt, and 1/2 teaspoon pepper and boil, uncovered, until vegetables are tender, 15 to 20 minutes. Discard thyme and bay leaves. Puree about 4 cups soup in a blender, in batches if necessary, until smooth (use caution when blending hot liquids). Return to pot and season with salt, pepper, and vinegar. Serve topped with crumbled bacon.