Preheat the oven to 425 degrees F. Spray 6 cups of a standard muffin tin with the cooking spray, sprinkle with granulated sugar to cover the entire cup and dust off any excess. This will prevent the lava cakes from sticking. Set aside.
Melt the chocolate and coconut oil together in a double boiler, 5 to 7 minutes. Remove from the heat, add the flour and salt and stir until combined. Whisk the eggs and egg yolks together in a small bowl and slowly add to the chocolate mixture. Stir in 1 teaspoon of the red food coloring.
In a small bowl, beat together the cream cheese, granulated sugar, vanilla extract and remaining 1 teaspoon red food coloring. Spoon the filling mixture into a disposable pastry or icing bag and make a small cut when ready to fill.
Using a heaping 1/4-cup scoop, divide the lava cake mixture among the prepared muffin cups. Fill the centers with about 1 1/2 tablespoons of the cream cheese mixture. Bake until the edges are firm but the centers are not set, 9 to 11 minutes. Cool for 2 to 3 minutes, invert and sprinkle with powdered sugar. Serve immediately. (To make ahead, bake for 8 minutes, invert and rewarm in the microwave for 1 minute. Dust with powdered sugar.)