Preheat oven to 350°.
To prepare muffins, lightly spoon flours into dry measuring cups; level with a knife. Combine flours, flaxseed, and next 4 ingredients (through salt) in a medium bowl, stirring with a whisk. Make a well in center of mixture.
Combine milk, orange juice, melted butter, vanilla, and eggs, stirring with a whisk; add to flour mixture, stirring just until moist. Fold in apple and raisins. Spoon batter into 18 muffin cups coated with cooking spray.
To prepare streusel, combine walnuts, 2 tablespoons brown sugar, and chilled butter in a small bowl, stirring with a fork until crumbly. Sprinkle streusel evenly over batter. Bake at 350° for 20 minutes or until muffins spring back when touched lightly in center. Remove from pans immediately; place on a wire rack. Serve warm or at room temperature.