Preheat the oven to 400 degrees F. Spray a 12-cup muffin tin with nonstick cooking spray.
Heat the canola oil in a large skillet or wok over medium-high heat. Add the onions, peppers and carrots and cook, stirring occasionally, until softened and slightly charred, 3 to 5 minutes. Stir in the peas and bean sprouts and cook another 2 minutes. Transfer to a large bowl and stir in the rice, scallions, chopped shrimp, soy sauce, sesame oil, eggs, flour, a pinch red pepper flakes and salt.
Spoon the rice mixture into the wells of the muffin tin, filling to the top and pressing gently with the back of a spoon. Top each with a whole shrimp and sprinkle the shrimp with salt and a pinch red pepper flakes. Bake until sides of the cups are golden and the shrimp is cooked through, 20 to 24 minutes.
Let sit 5 minutes, then remove the rice cups with a small offset spatula and top with sliced scallions. Serve with soy sauce for drizzling.