Melt unsalted butter in a medium saucepan over medium. Stir in flour, and cook, stirring constantly, 1 minute. Whisk in milk until smooth. Cook over medium, stirring constantly, until thickened to a thick gravy consistency, 2 to 3 minutes. Remove from heat, and stir in chipotle and salt. Set aside.
Heat oil in a medium skillet over medium-high. Add onion; cook, stirring often, until browned and tender, about 14 minutes. Remove from heat.
Assemble each sandwich in this order: 1 bread slice, 2 slices Petit Jesu, 1/3 cup grated cheese, 2 tablespoons chipotle mixture, 2 chopped prunes, salt to taste, 1 tablespoon cooked onions, 2 slices Petit Jesu, and 1 bread slice. Repeat with remaining ingredients to make 3 more sandwiches. Brush outside of bread with clarified butter.
Working in batches if necessary, place sandwiches in a preheated electric sandwich toaster, and cook until browned and cheese is melted, about 3 minutes.
