Preheat the oven to 425 degrees F.
For the soup:
Place the onions on a baking sheet and dress lightly with EVOO, and season liberally with the thyme and salt and pepper. Dress the garlic with EVOO, salt and pepper, and then wrap the garlic in foil and fold edges over to secure a pouch. Roast the onions until tender and golden, 30 minutes, turning once. Roast the garlic until very soft, 35 to 40 minutes.
Char the peppers over an open flame on the stovetop or under a hot broiler (once the onions and garlic are removed). Place the charred peppers in a bowl, cover and cool to handle. Wipe away the pepper skins with a towel. Seed and coarsely chop.
Cool the garlic to handle, and then squeeze the garlic cloves away from the skins and into a food processor bowl. In two batches, add the onions, garlic, peppers, stock and tomatoes. Puree until fairly smooth. Add the puree to a pot with the passata and season with the herbes de Provence and add the torn basil. Heat the soup through and simmer to thicken a little and combine flavors, about 20 minutes. Adjust the salt and pepper. Cool and refrigerate for a make-ahead meal.
For the grilled cheese croutons:
To serve, heat the soup over medium heat and preheat a griddle pan over medium heat. Butter all the bread on one side with the softened butter. Make the cheese sandwiches with the buttered sides facing out. Grill the sandwiches until golden and crisp on each side. Dice into bite-size squares. Serve the soup in shallow bowls and top each with a few grilled cheese croutons.