Start by making the crumble: melt the ghee and honey in a small pan and bring to a boil over medium-high heat. When it bubbles vigorously, add the chopped pecans and cook until the pecans take a nice golden caramel color and start to smell heavenly good, about 1-2 minutes. Remove to a plate and sprinkle with fleur de sel. Set aside to cool.
In a large mixing bowl, mix almond flour, tapioca starch, coconut flour, flaxseed meal, cinnamon, baking soda, cream of tartar and salt until fully incorporated. While sifting is not mandatory, I strongly recommend it. It's the best way to make sure all the lumps get broken down (coconut flour is especially lumpy) and any potential larger pieces or unwanted debris get caught.
In the bowl of your food processor, add the pecans, ghee and raw honey listed under the "wet ingredients" section. Process until well combined and paste-like in consistency.
Add the eggs, one at a time, processing until well incorporated between each addition. When the mixture is smooth and creamy, add the coconut milk and vanilla and resume processing until well incorporated.
Pour this over the reserved flour mixture and mix delicately with a wooden spoon or rubber spatula until well combined, without over-mixing the batter.
Divide evenly between prepared muffin cups; break the crumble down with your fingers and sprinkle over the muffins.
Bake in a 375F oven for about 20 minutes, or until a toothpick inserted in the center of a muffin comes out clean.