In a stockpot, set over low heat, combine 3 tablespoons of the olive oil, the onion, salt, and red pepper, and stir occasionally, but a minimum of 5 to 7 minutes, until the onion is softened, so the longer, the better. Add the garlic and cook until fragrant, about 2 minutes.

Add the beans and just enough stock to cover the mixture to an aggressive simmer until warmed through, about 3 minutes.

Remove the pot from the heat and, using a slotted spoon, scoop out and set aside about 1 cup of the beans. Stir the vinegar into the remaining soup using a handheld immersion blender. Set back on the stovetop over low heat to keep warm.

Preheat the broiler. Place the bread slices on a sheet pan and broil on the top rack of the oven just until toasted but not quite golden, don't burn. Flip them over, brush with the remaining 2 tablespoons olive oil, sprinkle with the Parmesan, and broil until the cheese has melted, another 1 ½ minutes. Remove from the oven.

Serve the soup in large shallow bowls, placing one giant crouton in the middle of the soup along with a few reserved beans, the pesto, scallions, and chives. Drizzle with more olive oil just before serving.