Cut the butternut squash in half and scoop out the guts and seeds with a spoon; wash the potatoes and cut them in half lengthwise. Place the vegetables in a broiler pan and drizzle their flesh with the melted coconut oil, then sprinkle liberally with salt and pepper.
Turn the squash and potatoes flesh side down and cover the pan with aluminum foil. Bake in the oven for about 40-45 minutes, until the vegetables become really soft and can easily be pierced with the tip of a sharp knife.
Meanwhile, melt 3 to 4 tablespoons of coconut oil in a heavy skillet set over medium-high heat. Add the plantain and cook, tossing gently from time to time, until the plantain becomes golden brown and fragrant, about 5 minutes total. Remove the plantain to a plate and sprinkle with salt.
Put the skillet back over the heat source, add about 2 tablespoons of coconut oil then throw in the onion; cook until softened and fragrant, about 2-3 minutes, then crank up the heat to high and add the ground beef. Break the meat into little pieces with a wooden spoon and sprinkle with the salt. Cook until the beef is no longer pink, and then add the coconut water. Continue cooking until the coconut water completely evaporates and the beef turns dark brown and starts to become crispy, about 12 to 15 minutes.
When the beef is cooked to your liking, lower the heat and add the coconut milk, garam masala, black pepper, cayenne pepper and crushed pili-pili (or chili pepper flakes). Mix well and continue cooking until the mixture is well combined and creamy, about 1 minute.
Transfer the meat to a baking dish and then top with the reserved plantain. Set aside.
When they are done baking, remove the butternut squash and sweet potatoes from the oven and let them cool for a few minutes, until you can safely handle them with your bare fingers. Scoop out the flesh of the butternut squash with a spoon and peel the sweet potatoes by gently pulling on the skin with your fingers; It should come right off.
Place the squash and potato flesh in the bowl of your food processor, along with the coconut milk, ghee, garam masala, salt and pepper. Process until reduced to a smooth puree; you may have to stop the motor and scrape the sides a few times.
Mound this puree on top of the plantains and spread it evenly all the way to the sides of the dish.
Bake in a 375F oven for 30 to 35 minutes, until the top starts to turn golden. For an even deeper golden coloration, drizzle a little bit of melted coconut oil over the top and place the dish under the broiler for a few minutes.
Allow your Shepherd’s Pie to rest and cool for 5 to 10 minutes before serving. Garnish with toasted coconut flakes if desired.