Heat oven to 400°. Line a standard 12-cup muffin tin with paper liners. In a large bowl, whisk together the flour, sugar, cocoa powder, baking soda, and kosher salt. Stir in chia seeds, ½ cup chopped almonds, and chocolate chips. In a separate medium bowl, whisk together the buttermilk, melted butter, egg, and almond extract. Add the wet mixture to the dry mixture and stir just until combined.
Divide the batter evenly among the muffin cups. Sprinkle each with 1½ to 2 teaspoons chopped almonds and a pinch of flaky sea salt, if desired. Bake until muffins spring back when lightly pressed, about 18 minutes. Let cool in pan. Serve immediately or keep in an airtight container for up to 3 days. Storage note: muffins can be transferred to plastic storage bags and frozen for up to one month.