Preheat oven to 350°F. Line a 12-cup muffin pan with cupcake liners. Set aside.
Add vinegar to almond milk in a small bowl. Stir and set aside. Meanwhile, place gluten free flour, cocoa, sugar, baking soda and salt in a large bowl. Whisk until combined. Pour milk mixture, plus the oil and vanilla into the bowl of dry ingredients. Stir until everything is incorporated and you have a smooth batter.
Pour batter into prepared pan and bake for 20-25 minutes or until a toothpick inserted into the center of a cupcake comes out clean. Let cool.
For the vanilla frosting (used for filling and squiggles on top)
Place the margarine and shortening in a large bowl. Beat with an electric mixer on medium until smooth and creamy. With mixer on low, gradually add powdered sugar, vanilla and salt. Once added, turn mixer up to medium and beat for a minute.
Scoop frosting into a pastry bag fitted with a #12 round pastry tip. Fill cupcakes with vanilla frosting by inserting tip into the middle of each cupcake and squeeze until frosting spills over the top. Spread the extra frosting over the top with an offset spatula. Refrigerate for an hour.
For the chocolate ganache
Place chocolate chips in a small microwave safe bowl. Microwave on high for 30 seconds. Stir. Repeat and stir again until completely smooth. Add oil and stir to combine. Dip chilled cupcakes into melted chocolate mixture. Refrigerate for 20 minutes. For the squiggles on top: Change pastry tip to a #5 round tip. Squeeze about 7 loops onto the top middle of the chilled, chocolate covered cupcake. Serve and enjoy. Store leftover cupcakes in the refrigerator.