Spray a 9-inch square baking dish with cooking spray. Place bread slices in a single layer in the bottom of the prepared baking dish.
Whisk milk, egg substitute, and chives together in a bowl; pour over bread slices into prepared baking dish. Sprinkle bacon crumbles over the top. Cover the dish with plastic wrap and refrigerate, 8 hours to overnight.
Remove and discard plastic wrap from baking dish; let dish come to room temperature, about 30 minutes.
Preheat oven to 350 degrees F (175 degrees C).
Bake casserole in the preheated oven for 40 minutes. Sprinkle cheese over the top and continue baking until cheese is melted and casserole is set, about 5 minutes more.