Preheat the oven to 375°F. Place the beets in a baking dish, and roast for an hour, or until you can easily pierce the vegetables with a knife or fork.
Reduce heat to 350°F for the cupcakes. Line 2 standard muffin tins for 16 cupcakes, or grease well with butter or coconut oil.
Once the beets have slightly cooled, peel the skins off. Cut into chunks, and place in a blender or food processor. Add water and kale, and blend until fully pureed. Set aside.
In a large mixing bowl, beat the applesauce, sugar, and honey together. Add eggs and vanilla, and mix well. Add the beet-kale puree, and stir with a wooden spoon to combine.
In a smaller mixing bowl, whisk the flour, cocoa powder, baking soda, baking powder, and salt. Add 1/2 the dry mixture to the wet ingredients, and stir to mix. Add 1 cup of milk, and mix. Add 1/4 more of the dry mixture, and stir. Add remaining milk, mixing to combine, and then incorporate the last of the dry. Be careful not to overmix.
Fill the muffin tins about 2/3 of the way full with batter. Bake for 18 minutes, or until a toothpick inserted in the center comes out clean of batter. Let cool completely.
To make the cream cheese frosting, beat together the Neufchatel, butter, and powdered sugar. Transfer to a pastry bag or zippered plastic bag, and snip off the end. Use to decorate the cupcakes, once they have had a chance to fully cool.