Preheat oven to 350 degrees F (175 degrees C). Grease an 8x8-inch baking pan.
Whisk melted butter with 1 cup sugar in a large mixing bowl; stir cocoa, red food coloring, 1 teaspoon vanilla extract, vinegar, and salt into butter mixture one at a time, mixing well after each addition to avoid lumps. Stir 2 eggs into mixture until thoroughly combined.
Stir flour into cocoa mixture just until combined; set aside 1/4 cup batter. Pour remaining batter into the prepared baking dish.
Beat cream cheese in a bowl using an electric mixer on medium speed until light and fluffy; beat 1/4 cup sugar, 1 egg, and 1/4 teaspoon vanilla extract into cream cheese until very well blended and only small lumps remain, 3 to 4 minutes.
Spoon cream cheese mixture in dollops over the batter in pan; gently smooth tops of dollops even with batter using a knife or offset spatula. Do not overmix. Drizzle reserved 1/4 cup of batter over the dollops of cream cheese mixture. Drag a knife or skewer through the batter and cream cheese mixture to create swirls.
Bake in the preheated oven until a toothpick inserted into the center of the pan comes out clean, 30 to 35 minutes. Cool completely before cutting into bars; store covered in refrigerator.