Place quinoa in a sieve and rinse under cold, running water for about 10 seconds. Place into a small pot, along with the water. Cover and set over high heat. Bring to a boil, reduce heat to as low as possible and cook for 20 minutes. Turn off heat and leave to steam for 5 minutes. Fluff with a fork. Set aside.
While quinoa is cooking, heat a large skillet over medium high heat. Add 2 tablespoons of oil to the pan. Add the onions and cook, stirring frequently, until very soft and light, golden brown, about 7-8 minutes. Add 1/2 teaspoon of the cumin seeds and season with a pinch of salt. Remove from pan and set aside.
Add another 2 tablespoons oil to the pan. Add the mushrooms to the pan. (If your pan is on the smaller side, you may have to saute' the mushrooms in two batches.) Cook, stirring frequently, until mushrooms are browned and softened. Add the remaining 1/2 teaspoon of cumin seeds, thyme and a season with salt. Add the balsamic vinegar. It should sizzle and cook off to almost nothing left in the pan.
Stir in the cooked quinoa, onions, dill, feta and red chili flakes. Toss to combine. Season with salt and pepper. Taste. Add up to 2 more tablespoons of balsamic for more acidity, if desired. Serve warm.