Pre-heat the oven to 375 degrees (F). Slice open the pumpkin and butternut squash, remove seeds, and place facedown on a pan lined with parchment paper and bake for 20-30 minutes until you can easily pierce the skin with a fork. Remove and allow to cool or store in the refrigerator until ready to bake (up to 3 days). Reduce temperature to 350 F.
In a medium sized bowl, mix together the flour, baking soda, baking powder, salt, and all the spices.
In the bowl of a standing mixer add the mashed pumpkin and squash and sugars. Mix until smooth and creamy (about 3 minutes).
Add the eggs, one at a time, and the vanilla powder. Mix well (about 1 minute).
Add the oil and mix until smooth (about 1 minute)
Slowly fold in the flour mixture, careful not over mix.
Add in any optional mix-ins you choose such as nuts, chocolate, oats, at this step.
With a scoop, fill the cavities of a cupcake pan or muffin pan.
Bake for 13-15 minutes, or until a toothpick comes out clean. The tops should puff up and be firm in the center.