Combine milk, stock, cauliflower, potato, onion, garlic, and thyme in a large saucepan. Season with salt and pepper. Bring to a boil over medium-high heat; reduce heat and simmer, partially covered, until the vegetables are very tender, 18 to 20 minutes.
Meanwhile, melt butter in a large skillet over medium heat. Cook, swirling occasionally, until golden brown, 2 to 4 minutes. Add bread and cook, stirring often, until toasted, 10 to 12 minutes. Season with salt and pepper.
Discard thyme sprigs. Puree soup, in batches, in a blender until smooth. Add cream and pulse to combine. Season with salt and pepper.
Serve topped with croutons, pomegranate seeds, and chives.