Preheat oven to 350 degrees. Line cupcake tins with liners.
In a large bowl, whisk together flours, cocoa and salt.
In another large mixing bowl, beat sugar, applesauce and oil until combined. Add eggs and egg whites, one at a time, beating until each is incorporated, scraping down sides of bowl as needed. Mix in food coloring and vanilla.
Add flour mixture in three batches, alternating with two additions of buttermilk (a half a cup each time), and whisking well after each.
Stir together the baking soda and vinegar in a small bowl (it will foam); add mixture to the batter, and mix until combined, about 10 seconds.
Divide batter evenly among lined cups, filling each three-quarters full. Bake, rotating tins halfway through, until a toothpick inserted in centers comes out clean, about 20 minutes. Mix frosting ingredients together in a bowl (you can use a beater to speed it up).
Let cupcakes cool completely, then frost with low-fat cream cheese frosting.