Preheat oven to 450°F and line a baking sheet with parchment paper; set aside.
In a small saucepan, bring the almond milk and vanilla extract to a boil over high heat.
Add the uncooked quinoa, stir, reduce heat to low, cover, and simmer until the liquid is absorbed, about 25 minutes.
In a medium bowl, toss the cubed apricots, halved cherries, and 1/2 tablespoon honey; spread the fruit on the prepared baking sheet and roast at 450°F until juices release and fruit lightly browns, about 13–15 minutes.
When the quinoa is cooked, transfer it to a medium bowl, stir in cardamom and a pinch of sea salt, then refrigerate until slightly cooled.
Lower oven temperature to 425°F and generously spray a 12-cavity muffin tin with cooking spray.
In a large microwave-safe bowl, melt the almond butter until smooth (about 1 minute). Stir in the remaining 3 tablespoons honey and the minced fresh ginger.
Add the slightly cooled quinoa to the almond butter mixture and mix until well combined.
In a separate bowl, whisk together the 2 whole eggs and the egg whites from 2 eggs, then pour into the quinoa mixture and stir until combined; the batter will be slightly soupy.
Divide the mixture among 11 muffin cavities, filling each about halfway, then evenly divide the roasted fruit among the muffins and sprinkle tops with minced pistachios.
Bake at 425°F until muffins have risen and tops are set, about 12–14 minutes.
Immediately remove muffins from the tin with a sharp knife and transfer to a cooling rack to cool completely; drizzle with additional almond butter if desired before serving.