Cook the quinoa according to package directions. Set aside for serving.
While the quinoa cooks, place the salmon in a small, shallow dish so that the pieces are nearly touching but do not overlap too much. In a medium bowl or large measuring cup, stir together the soy sauce, rice vinegar, honey, garlic, ginger, and red pepper flakes. Pour two-thirds of the mixture over the salmon, reserving the remaining one-third. Let the salmon marinate at room temperature for 15 minutes, flipping once halfway through.
In the meantime, in a large nonstick skillet, heat 1 tablespoon olive oil over medium high. Add the vegetables and white/light green parts of the scallions. Sauté until crisp-tender, about 8 to 10 minutes. The timing will vary based upon the veggies you use; harder veggies like diced carrots will need longer, while softer veggies like bell peppers and broccoli will cook more quickly. If you are using frozen veggies, they should all cook in the same amount of time. Add the edamame and 2 tablespoons of the reserved marinade and cook 30 additional seconds. Remove to a plate or bowl and cover to keep warm.
With a paper towel, carefully wipe the skillet clean. Add the remaining 1 tablespoon olive oil and increase the heat to high. Once the oil is hot and shimmering, add the salmon and 2 tablespoons of the remaining marinade to the skillet (discard the salmon marinade left in the dish).
Let cook 2 minutes undisturbed, then turn the salmon pieces and continue cooking 2 to 3 additional minutes, just until the salmon is cooked through. (Do not overcook or the salmon will be dry.)
To serve, place the cooked quinoa in individual serving bowls. Top with sautéed veggies, salmon, and reserved dark green onions. If desired, sprinkle with a little of the remaining reserved marinade and additional red pepper flakes. Enjoy immediately.