Preheat oven to 350°F (175°C) and line two 12-cup muffin pans with cupcake liners.
In a large bowl, whisk together flour, sugar, cocoa powder, baking soda, baking powder, and salt until well combined.
In a medium bowl, whisk together buttermilk, oil, eggs, red food coloring, vanilla extract, white vinegar, and apple cider vinegar until smooth and evenly colored.
Pour wet ingredients into dry ingredients and fold gently just until combined with no flour streaks. Don't overmix.
Fill each cupcake liner about 2/3 full using an ice cream scoop or 1/4 cup measure.
Bake for 18-20 minutes, rotating pans halfway through, until a toothpick inserted in center comes out with just a few moist crumbs.
Let cupcakes cool in pans for 5 minutes, then transfer to wire racks to cool completely, about 45-60 minutes.
Beat softened cream cheese and butter with electric mixer on medium speed for 2-3 minutes until smooth and fluffy.
Add vanilla and salt, then gradually add sifted powdered sugar one cup at a time, beating until light and fluffy.
Frost cooled cupcakes using a knife, offset spatula, or piping bag fitted with a star tip. Refrigerate 20-30 minutes to set.