Preheat oven to 350ºF and line muffin pans with cupcake liners.
Whisk together milk and apple cider vinegar and set aside to curdle, about 5 - 10 minutes. If it doesn't curdle, that's OK!
Sift together the flour, sugar, cocoa, baking powder, baking soda, and salt into large bowl and mix.
Add the oil, food coloring, vanilla extract, and almond extract to the curdled milk-vinegar mixture. Whisk well to combine. Gently fold wet ingredients into dry, mixing until large lumps disappear.
Fill cupcake liners about two-thirds full (these cupcakes will rise fairly high). Place in preheated oven and bake 18 to 20 minutes, but be sure not to over-bake. Use a toothpick inserted in the center to tell--the toothpick will be red, but there should not be any batter or crumbs sticking. When done, let cool for a few minutes then transfer cupcakes to cooling rack to cool completely.
Make the cream cheese frosting: in the bowl of a standing mixer (or use a large bowl with a hand mixer), combine cream cheese and butter. Beat on medium speed until smooth. Pour in vanilla extract, then add in the powdered sugar, about 1-2 cups at a time. Beat on medium speed until completely incorporated after each addition. Refrigerate until ready to use.
Frost with cream cheese frosting. These look especially awesome with a piped swirl! Try a Wilton 2A round tip to achieve a perfect swirl.