Preheat your oven to 355 ºF (180 ºC) and prepare a 12-cup muffin pan by lining it with cupcake liners.
In a large mixing bowl, sift together the gluten-free flour blend, almond flour, xanthan gum, baking powder, light brown sugar, and salt.
Add the softened butter to the dry ingredients. Using a hand mixer or a stand mixer fitted with the paddle attachment, blend until the butter is incorporated and the mixture resembles coarse crumbs or pea-sized pieces.
In a separate bowl, whisk together the room temperature milk, eggs, lemon juice, and vanilla paste until the mixture is smooth and uniform.
Pour the wet ingredients into the dry mixture, whisking until a smooth, lump-free batter forms.
Fill each cupcake liner with a tablespoon of batter, sprinkle a few chocolate chips on top, and add another layer of batter. Continue alternating batter and chocolate chips until the liners are about three-quarters full, ensuring even distribution to keep the chocolate chips from sinking.
Bake the cupcakes for approximately 25 minutes, or until a toothpick inserted into the center comes out clean and the tops are lightly golden and slightly domed.
Once baked, remove from the oven and allow the cupcakes to cool completely before frosting.