Heat the oven to 350°F and line a 12-cup muffin tin with paper or silicone liners.
In a medium bowl whisk together the mashed sweet potato, almond milk, eggs, maple syrup, melted coconut oil and vanilla until smooth and uniform. Set aside for 5 minutes to hydrate the flours.
Whisk the oat flour, almond flour, cinnamon, ground ginger, baking powder, baking soda and sea salt in a separate bowl until evenly combined.
Fold the dry mixture into the sweet potato mixture using a spatula until just combined — scrape the bowl and fold gently so the batter stays tender. A few small lumps are fine; avoid overmixing.
Spoon the batter into the prepared muffin cups, filling each about three-quarters full. Smooth the tops with the back of a spoon.
Bake on the center rack for 18 minutes, rotating the pan once halfway through to ensure even browning. A toothpick inserted near the center should come out with a few moist crumbs.
Remove the tin from the oven and let the cupcakes rest in the pan for 4–5 minutes, then transfer the cupcakes to a wire rack to cool completely (about 20–30 minutes). Frosting adheres best when the cupcakes are fully cool.
While the cupcakes cool, make the frosting: beat the softened cream cheese until smooth in a medium bowl, then add the Greek yogurt, maple syrup and vanilla. Whip on medium speed until fluffy and homogenous, scraping the bowl once or twice. Taste and adjust maple for sweetness if desired.
Chill the frosting 10 minutes if it seems loose. When cupcakes are completely cool, spread or pipe the frosting over each cupcake. Optionally garnish with a light dusting of cinnamon or a small sprinkle of chopped toasted pecans.