Preheat your oven to 450°F (for the initial heat boost). In a large mixing bowl, combine 1/3 cup Greek yogurt, 1/3 cup avocado oil, 2/3 cup cane sugar, 1/4 cup milk, 2 teaspoons vanilla extract, and 1/4 teaspoon almond extract. Whisk until smooth and well combined. Add 3 eggs and whisk again until the mixture is completely smooth.
To the same bowl, add 1-1/2 cups almond flour, 1/2 cup vanilla protein powder, 3/4 cup all-purpose flour (or gluten-free flour blend), 1-1/2 teaspoons baking powder, and 1/2 teaspoon baking soda. Whisk gently until just combined and no dry spots remain. Be careful not to overmix, as this can make the muffins tough.
Add 1 cup of chocolate chunks to the batter and fold gently with a spatula until evenly distributed throughout the batter.
Line a 12-cup muffin tin with paper liners and spray them lightly with non-stick spray. Fill each cup almost to the top, allowing the batter to mound slightly in the middle for that bakery-style dome. Finely chop 1/4 cup pistachios and sprinkle them generously over the tops of the muffins. If desired, press a few additional chocolate chunks into the tops.
Bake at 450°F for the first 5 minutes (this initial high heat helps create those beautiful domed tops), then reduce the temperature to 350°F without opening the oven door. Continue baking for 12-15 minutes or until the muffins are lightly golden around the edges and a toothpick inserted in the center comes out with just a few moist crumbs. Be careful not to overbake.
Allow the muffins to cool in the pan for 5 minutes, then transfer to a wire rack to cool completely. Meanwhile, prepare the glaze by mixing 1/2 cup powdered cane sugar with 1/4 teaspoon vanilla extract and 1 tablespoon milk. Add more milk, a little at a time if needed, until you reach a thick but pourable consistency. Drizzle the glaze over the cooled muffins and allow it to set before serving.