Make the cupcakes. Preheat the oven to 350°F. Line a muffin tin with cupcake liners.
In a medium bowl, whisk together the almond milk and apple cider vinegar.
In a separate large bowl or stand mixer, mix the almond flour, coconut sugar, coconut flour, tapioca starch, baking powder, baking soda, and salt. Stir to blend.
To the medium bowl with the milk and vinegar mixture, whisk in the eggs, applesauce, maple syrup, and vanilla extract until creamy.
Pour the wet ingredients into the bowl with the flour mixture and beat until a batter is formed. Let the batter rest in the bowl for 10 to 15 minutes.
Evenly distribute the batter between the cupcake liners, filling them about 3/4 of the way to the top. Bake for 22 to 25 minutes until a toothpick inserted into the center comes out clean. Allow the cupcakes to completely cool in the muffin tin before incorporating the custard and frosting.
Make the custard. In a small saucepan over medium heat, slightly warm the coconut cream, about 1 minute. Add the gelatin and whisk vigorously until dissolved. Bring to a simmer. If there are still clumps, that is OK, they should dissolve eventually.
Meanwhile, whisk together the egg yolks and powdered sugar. Once the coconut cream and gelatin mixture is simmering, add half to the yolk and sugar mixture and whisk to combine. Pour it back into the saucepan and whisk until everything is creamy. Continue to cook until slightly reduced, whisking constantly, about 4 minutes. Be sure to watch the saucepan, the mixture can heat quickly and the egg can curdle.
Remove from heat and whisk in the butter and vanilla extract. Add the arrowroot starch and whisk vigorously until dissolved. Alternatively, if there are still clumps, you can transfer the mixture to a blender and process until smooth. Transfer the mixture to a small glass or ceramic bowl. Allow to cool about 1 hour until thickened, stirring occasionally (**see note). Use immediately.
To make the frosting, combine the coconut oil and butter (or vegan butter) in a large bowl. Beat with a hand mixer or immersion blender with the whisk tool until fluffy, about 30 seconds.
Add the cacao powder or cocoa powder, and powdered monk fruit and beat again until everything is combined. Use a spatula to scrape down the sides as you need to.
Using a spatula, mix the frosting. Use immediately, or place in the refrigerator for 10 minutes for a denser texture.
To assemble the cupcakes: once the cupcakes have completely cooled, use a 1-inch biscuit/cookie cutter to cut a hole in the center. You can also use a knife to create a well. Reserve the top. Transfer about a tablespoon or so of the custard into the center of the cupcake, and place the top back on. Spoon frosting on top or use a piping bag to frost.