Melt 1 1/2 tablespoons butter in a small saucepan over medium heat. Add flour slowly, stirring until it forms a thick paste, about 4 minutes. Whisk milk into the paste until smooth with a gravy consistency, about 5 minutes. Stir in 1/2 teaspoon black pepper.
Melt 1 tablespoon butter and olive oil in a large skillet over medium-high heat. Saute red onion, garlic, red pepper flakes, and 1/2 teaspoon black pepper until onion is browned, about 6 minutes.
Mix collard greens into the skillet, in batches if necessary. Cook and stir until slightly wilted and all greens fit in the skillet, about 2 minutes. Add balsamic vinegar; reduce heat to medium-low. Cook, stirring occasionally, until greens are bright green and tender, 5 to 10 minutes more. Add enough gravy mixture to just coat the greens.
Transfer cooked greens to a baking dish small enough so the greens can be piled 1 to 1 1/2 inches deep. Cover with French fried onions and press into the dish.
Bake in the preheated oven until fried onions brown slightly, 20 to 30 minutes.