Preheat the oven to 425°F. Line a baking sheet with parchment paper and set aside.
In a small pot, combine 2/3 cup unsweetened vanilla almond milk and 1 teaspoon vanilla extract. Bring to a boil over medium-high heat.
Add 1/3 cup uncooked quinoa to the boiling almond milk, stir, reduce heat to low, cover, and simmer until the quinoa has absorbed all the liquid, about 25 minutes. Remove from heat.
While the quinoa cooks, in a medium bowl toss 3/4 cup cubed apricot (125 g), 1/2 cup pitted and halved cherries (90 g) and 1/2 tablespoon of the honey. Spread the fruit in a single layer on the prepared baking sheet.
Roast the fruit in the preheated oven until it releases its juices and begins to lightly brown, about 13 to 15 minutes. Remove from oven and set aside to cool slightly.
Transfer the cooked quinoa to a medium bowl. Stir in 1 teaspoon ground cardamom and 1 pinch sea salt. Refrigerate the quinoa until it has cooled (cool to the touch) before proceeding.
Generously spray a 12-cavity muffin tin with cooking spray and set aside.
In a large microwave-safe bowl, place 1/4 cup natural almond butter and microwave until it becomes smooth and pourable, about 1 minute. Stir in the remaining 3 tablespoons honey and 1/2 teaspoon minced fresh ginger until combined.
Stir the slightly cooled quinoa into the almond butter mixture until well combined.
In a separate medium bowl, whisk together 2 large eggs and the egg whites from 2 eggs until blended. Pour the eggs into the quinoa mixture and stir until evenly combined; the batter will be slightly soupy.
Divide the quinoa batter evenly among the 12 muffin cavities, filling each cavity only halfway.
Evenly divide the roasted apricot and cherry mixture among the muffin cavities, placing the fruit on top of the batter. Sprinkle 3 tablespoons minced pistachios over the tops of the muffins.
Bake in the preheated 425°F oven until the muffins have risen and the tops are set, about 12 to 14 minutes.
Remove the muffin tin from the oven. Immediately run a sharp knife around each muffin to loosen the edges, then lift the muffins out of the tin and transfer them to a cooling rack to cool completely.
If desired, drizzle additional natural almond butter over the cooled muffins before serving.