Preheat oven to 350°F. Line a 12-count muffin tin with paper liners. Set aside.
Combine flour, baking soda, baking powder, cinnamon, and salt. Set aside.
In a large bowl, whisk oil, applesauce, brown sugar, granulated sugar, eggs, and vanilla extract until thoroughly combined. Add dry ingredients and whisk until just combined. Stir in carrots using a rubber spatula or spoon.
Divide batter evenly among 12 muffin cups (I use an ice cream scoop). Bake for 18-20 minutes, until a toothpick inserted into the center comes out clean. These cupcakes do not have a high rise, they'll be just over the top of the paper liner. Cool for 10 minutes, then remove cupcakes to a wire rack to cool completely.
Place the butter, cream cheese, brown sugar, and molasses in the bowl of a stand mixer fitted with the paddle attachment. Beat for 1-2 minutes at medium speed. If necessary, scrape the sides of the bowl and the beater, then beat a little longer. Let this mixture sit for 5 minutes, to allow the brown sugar to absorb into the wet ingredients (this is to avoid grittiness).
Add the powdered sugar and vanilla and beat until smooth and creamy, scraping the beater and sides of the bowl periodically. If you prefer the frosting thicker, add a little more powdered sugar. Give it a mix on high speed for one full minute. This frosting is on the softer side and it will firm up once refrigerated.
Spread or pipe the frosting on top of each cupcake (I used a pastry bag and open star decorating tip). Place the cupcakes in the fridge so the frosting can firm up a bit. Serve at cool room temperature.