Adjust oven rack to lower-middle position and heat oven to 375 degrees. Mix flours, baking powder, baking soda, salt, and cinnamon in a medium bowl.
Beat coconut oil, sugar, and molasses with an electric mixer over medium-high speed until light and fluffy, a minute or so. Beat in chia seed mixture, then 1/2 of the dry ingredients, followed by 1/3 of the yogurt. Continue beating in dry ingredients, alternating with yogurt, in two more rounds to make a stiff batter. Switch to a rubber spatula and fold in the apples and walnuts.
Spray a 12-cup muffin tin with vegetable cooking spray. Use a large ice cream scoop to divide batter evenly among the cups. (They will be full.) (If using crumble topping, sprinkle it on now.) Bake until muffins are golden brown, about 30 minutes. Set on a wire rack to cool slightly, about 5 minutes. Remove muffins from tin and serve warm.