Place the bacon in a large, deep skillet and cook over medium-high heat until evenly browned, about 5 minutes per side. Drain the bacon slices on a paper towel-lined plate. Crumble once cooled.
Preheat an oven to 200 degrees F (95 degrees C) to keep the finished waffles warm. Preheat a waffle iron and coat lightly with cooking spray.
Combine the all-purpose flour, whole wheat flour, Parmesan cheese, parsley, rosemary, basil, sugar, baking powder, baking soda, and salt in a bowl. Whisk the milk, eggs, butter, and Dijon mustard together in a small bowl. Pour the wet mixture into the dry mixture and stir until just combined.
Pour about 1/3 cup batter into each square of the preheated waffle iron; cook until golden, 3 to 4 minutes. Keep prepared waffles in the preheated oven until all are cooked.
Stir the sour cream, sugar, and onion together in a small bowl. Drizzle the onion sauce evenly over the warm waffles. Sprinkle crumbled bacon over the waffles to serve.