Preheat oven to 350°. Line muffin tins with muffin liners.
Whisk almond flour, baking soda, and cocoa powder in a medium bowl; set aside.
Heat chocolate in a medium heatproof bowl set over a saucepan of simmering water, stirring occasionally, until melted. Remove bowl from heat. Stir in oil, vinegar, almond extract, and applesauce until smooth.
Beat eggs, coconut sugar + maple syrup mixture and salt in a stand mixer fitted with the whisk attachment on medium-high speed (or use an electric mixer and large bowl) until more than doubled in volume and mixture holds a ribbon for several seconds when the beater is lifted above batter, about 6–8 minutes. This step is very important because it is key to creating an aerated texture.
Pour the chocolate-applesauce mixture into egg mixture and beat on low speed until combined. Add in the dry ingredients and beat on lowest speed, scraping down bowl as needed, until combined.
Transfer batter to prepared muffin tins. Bake until the top springs back when gently pressed, 15-18 minutes.
Remove from the oven and let cool completely while you make the glaze.