Turn on your broiler and position the rack 8-10 inches from the heat. Place your tomatoes on a baking sheet along with the garlic cloves, unpeeled, and roast until charred, a few minutes per side. Watch the garlic carefully and move it to a spot on the baking sheet with more indirect heat if it becomes browned too quickly. Remove from the oven and when cool enough to handle, slip the skins from the tomatoes, remove the core and chop, and peel the garlic.
In a medium saucepan, melt the butter over medium heat. Add the onions and a teaspoon of salt and cook until softened, 10-12 minutes. Add the cumin, thyme and paprika and cook, stirring, 1 minute. Dump in the tomatoes and any juices, peppers and garlic cloves and chicken broth. Cook over medium heat at a simmer for 20 minutes.
Transfer the mixture to a blender. Be very careful when blending hot liquids. Hold a dishtowel firmly over top of the blender, or wait for it to cool down, or else it could explode. Let it blend until very smooth, then return to the pot. You may need to do this in two batches, depending on your blender size.
Keep the soup warm, tasting for seasoning and adding more salt and pepper if needed.
In a small bowl, mix the yogurt and harissa and a pinch of salt. When ready to serve, ladle the soup into bowls and top with a dollop of the yogurt harissa.