Stir 3 tablespoons flax meal with 1/2 cup of the warm water in a small bowl until combined; refrigerate at least 15 minutes to make a flax "egg".
Preheat the oven to 375°F (190°C) and grease a 12-cup muffin tin with a little coconut oil.
Spread 1/2 cup unsweetened coconut flakes on a small baking sheet and toast in the oven 2–4 minutes until golden, watching closely; set aside for topping.
In a large bowl, whisk together 1 1/2 cups oat flour, 1/2 cup vanilla-chai protein powder, 2 1/2 tsp cinnamon, 2 1/2 tsp cardamom, 1 1/2 tsp ginger, 1 1/2 tsp allspice, 1/2 tsp clove, and 1/2 tsp salt.
In another large bowl, whisk 2 tablespoons melted coconut oil with 4 tablespoons of the remaining warm water and 3 tablespoons plus 1 teaspoon baking powder until slightly foamy.
Add the remaining 1/4 cup melted coconut oil, the rest of the warm water, 2/3 cup coconut sugar, 2/3 cup applesauce, 1/4 cup agave, and 1 tablespoon vanilla extract to the bowl; beat with an electric hand mixer until combined.
Stir the chilled flax egg into the wet mixture, then fold the dry ingredients into the wet until a thick batter forms.
Spoon the batter into the prepared muffin tin, filling each cup about 3/4 full, and sprinkle toasted coconut flakes on top of each muffin.
Bake until lightly golden and a toothpick inserted into the center comes out clean, about 13–14 minutes.
Let the muffins cool in the pan to room temperature, then transfer to a wire rack to cool completely before serving.