Preheat oven to 350 degrees Fahrenheit (or 375˚F for high altitude). Place paper cups inside muffin/cupcake pan(s). Set aside.
Sift the flour, baking powder, baking soda, and salt into a bowl. Set aside.
In a separate bowl, whisk together the sugar and oil. Add the eggs one at a time, whisking until incorporated after each addition.
Add the coconut milk, coconut extract, and finely chopped sweetened coconut flakes. Mix to combine.
Add the flour mixture to the wet mixture. Stir until just combined.
Use a #24 scoop to fill paper-lined muffin cups 2/3 full with batter.
Bake the coconut cupcakes at 350 degrees Fahrenheit (or 375˚F for high altitude) for 15-18 minutes until the cake springs back when touched, or a toothpick inserted into the center comes out clean or with a few moist crumbs.
Transfer cupcakes to a wire rack to cool completely. Then top with frosting and toasted or regular coconut, as desired.
To toast shredded coconut: Simply place sweetened coconut flakes in a skillet over medium-low heat, stirring constantly, until golden brown. This will happen quickly, once it starts to brown. Remove promptly and empty toasted coconut into a heat-safe dish to prevent further carry-over cooking.
Store unfrosted cupcakes in an airtight container at room temperature up to 5 days.
Cupcakes topped with cream cheese frosting should be stored in an airtight container in the fridge up to 3-4 days. Be sure to let the cupcakes sit out at room temperature for at least 30 minutes before consuming, to take the chill off the cake.