Preheat oven to 350 degrees F (175 degrees C). Grease 2 muffin pans.
Whisk warm water and flaxseed together in a large bowl. Mix in sugar, applesauce, oil, and vanilla extract. Stir in zucchini until well combined.
Sift oat flour, all-purpose flour, baking powder, cinnamon, nutmeg, salt, and baking soda into a bowl. Stir in raisins and combine with the zucchini mixture until batter is just mixed.
Transfer batter into muffin cups using 1/4 cup measure.
Bake in the preheated oven until a knife inserted into a muffin comes out clean, 50 to 55 minutes.