Preheat the oven to 350°F (175°C). Line two 12-cup muffin tins with paper liners.
In a large bowl, whisk together the yellow cake mix, ground ginger, cinnamon, and allspice.
Add the molasses, 1 teaspoon vanilla, melted butter, milk, and eggs to the dry ingredients. Beat with a mixer on low speed until just combined, then increase to medium speed for 1 minute. Do not overmix.
Divide the batter evenly among the prepared cupcake liners, filling each about three-quarters full.
Bake for 18 to 22 minutes, or until a wooden skewer inserted into the center of a cupcake comes out clean. Let cool in the tins for 5 minutes before transferring to a wire rack to cool completely.
To make the frosting, beat the softened butter in a large bowl with an electric mixer on medium-high speed until light and fluffy, about 4 minutes. Gradually add the powdered sugar, one cup at a time, mixing on low speed until incorporated.
Add 1 teaspoon vanilla and the jellied cranberry sauce to the frosting. Beat on medium-high speed for another 2-3 minutes until the frosting is smooth and creamy.
Once the cupcakes are completely cool, use a small knife or an apple corer to remove a small cone from the center of each cupcake. Spoon about 2 teaspoons of the whole berry cranberry sauce into each cavity.
Pipe or spread the cranberry frosting over the filled cupcakes. Garnish with sugared cranberries or crushed gingerbread cookies, if desired.