Preheat the oven to 375 degrees F. Line two 12-cup muffin pans with cupcake liners and set aside.
Crack the eggs into a small container and set aside. Set the sugar aside. Then, in a small bowl, mix the gluten-free flour, nutmeg and salt together with a fork and set aside.
In the bowl of a stand mixer on medium speed, beat the butter with a paddle attachment until the butter is light in color and fluffy. Add the sugar to the butter and continue beating until the sugar is uniformly incorporated into the butter. Stop the mixer and scrape down the sides of the bowl. Then restart the mixer on low speed and add 1 egg at a time, waiting until it is fully incorporated in the butter mixture before adding the next egg.
Once all the eggs have been added, stop the mixer and scrape down the sides of the bowl to ensure that all the butter is incorporated with the eggs. Add the dry ingredients in three additions, alternating with the milk and oil, added in two additions, fully incorporating each addition into the batter before moving to the next step. If needed, stop the mixer after each addition and scrape down the sides of the bowl, and then resume mixing on low. Once all the dry ingredients and the milk have been combined with the butter mixture, evenly fill the cupcake pan cavities two-thirds of the way. Bake the cupcakes until the top of each cupcake is slightly springy to the touch and a toothpick inserted in the center comes out clean, 14 to 16 minutes. Remove from the oven and immediately turn the cupcakes out of the pan onto a cooling rack. Let the cupcakes cool completely.
Putting it all together: Using an apple corer or knife, core the centers out of the cooled cupcakes and remove. Fill the cupcakes with the Vanilla Bean Pastry Cream. Pipe the Dark Chocolate Italian Meringue Buttercream to cover the top of each cooled cupcake.
Bring the shallow dish or container for the finished pastry cream near the stovetop, and have the plastic wrap nearby as well. Measure the butter and vanilla bean paste into a small container and bring over near the stovetop. Pour the milk and 1/4 cup sugar into a heavy saucepot and scald over medium heat until the milk starts to steam. Do not boil the milk!
Meanwhile, whisk together the cornstarch and the remaining 1/4 cup sugar to combine and prevent any lumps in the cornstarch, and then add the whole egg and egg yolks. Whisk the egg yolk mixture until smooth and completely combined, and then bring over to the stove area and set the bowl with the yolks on top of a damp dish towel.
When the milk is steaming, remove from the heat. Whisking the egg yolk mixture constantly, slowly pour the milk in a steady stream into the egg yolk mixture. Once all the milk is combined with the egg yolk mixture, pour it back into the saucepot and return to medium-high heat, whisking constantly. Continue whisking and bring it to a boil. Let the egg yolk mixture boil for 1 minute (and continue whisking constantly so lumps don't form!) and then remove from the heat. Stir in the butter and vanilla bean paste, and then pour the entire contents of the pot into the shallow dish.
Immediately cover the surface of the pastry cream with the plastic wrap and refrigerate until cool, about 1 hour. Once cool, remove from the refrigerator and whisk until completely smooth and lump free. Fill a piping bag with the pastry cream and set aside until you need it.
Measure the sugar and 1/4 cup water into a heavy saucepan and heat over high heat until the sugar mixture reaches 250 degrees F, 15 to 20 minutes (use a candy thermometer to gauge the temperature).
While the sugar is cooking, beat the egg whites on medium speed in the mixing bowl of a stand mixture to the soft peak stage (whites will look foamy and white). Be careful not to over whip the whites (if the egg whites start to look clumpy, then they've been over whipped. If this happens, toss them out and start again! If the whites are beating faster than the sugar is cooking, turn down the mixer speed. You can always turn up the speed if you need to!) Add the cream of tartar and continue whipping.
While the egg whites are whipping on medium speed, gently pour the sugar syrup down the side of the mixing bowl. Turn the speed up to high and whip until the mixing bowl no longer feels warm to the touch, about 7 minutes.
Meanwhile, melt the dark chocolate in a microwave-safe bowl at 30 second intervals, stirring in between each interval, until the chocolate is completely melted.
Turn the mixer speed back to medium and add the butter in small chunks until it is completely incorporated. Stop the mixer, scrape down the sides of the bowl and add the vanilla bean paste and sea salt. Turn the mixer back on medium-low speed until the vanilla paste has mixed entirely through the buttercream. Spoon a small amount (about 1/2 cup) of the buttercream into the melted dark chocolate and stir to combine. Add the chocolate mixture back to the buttercream and whip thoroughly, stopping the mixer to scrape down the sides of the bowl to make sure all the chocolate is combined.
Fit an 18-inch plastic piping bag with an 847 star tip and twist the bag right by the tip to prevent the buttercream from leaking out. While you grasp the piping bag right above the star tip with your hand, fold the top of the piping bag over your hand and spoon the butter cream into the piping bag.
To bump up the chocolate flavor, you can melt 4 ounces good-quality dark chocolate and stripe the top of the frosted cupcakes with the dark chocolate.
This recipe was created by a contestant during a cooking competition. It has not been tested for home use.