Preheat oven to 350F. Spray or butter 2 12-cup muffin pans.
Whisk the flour, baking soda, salt and nutmeg together.
In the bowl of a stand mixer, beat the butter until creamy. Add the sugars and beat for a couple minutes, then add the eggs one at a time, beating well after each addition. Add vanilla and rum. Batter will be silky smooth. Lower the speed of the mixer and add the bananas. Do not be concerned when the banana curdles the batter.
Add the dry and liquid ingredients alternatively, beginning and ending with dry ingredients. Switch to a rubber spatula and stir in toasted coconut.
Using two 12-cup muffin tins, divide the batter event for a total of 24 cupcakes. Place the muffin tins on baking sheets and bake for 25 minutes, or until tops spring back when gently touched with your finger.
Cool on rack for 10 minutes, then remove from pans to cool completely.
To make the frosting:
Soften the cream cheese and butter, but don’t let it get warm, just take the chill off. Beat the cream cheese and butter together until creamy. Slowly add the powdered sugar until completely combined. Beat in the vanilla. Keep refrigerated until ready to use.