For the soup: Preheat the oven to 400 degrees F. Line a large baking sheet with nonstick aluminum foil.
Drizzle some olive oil in a zig-zag motion on the foil. Add the thyme and garlic and season the baking sheet with salt and pepper. Place the tomatoes, bell peppers and jalapeno on the baking sheet sliced-side down, covering the garlic cloves and thyme as you go along. Pour over the onions, drizzle the top of everything with olive oil and season again with a pinch of salt and a few grinds of pepper. Roast until the onions are golden and slightly charred, about 40 minutes.
Transfer everything from the baking sheet to a blender in batches and pulse until smooth. Pour into a pot and bring to a simmer over medium-high heat, stirring the entire time. Add enough vegetable stock to achieve the desired consistency; you may not use it all. Keep warm on low.
For the toast: Preheat the broiler on high.
Put a cooling rack on top of a baking sheet and arrange the bread on the rack. Top each piece of bread with a slice of cheese and place under the broiler. WATCH while they cook: the cheese will melt and bubble, then the corners will begin to blacken--pull them out then! This takes less than a minute. Serve aside or atop a bowl of soup.