Preheat oven to 350 ℉. Heat a large skillet over medium heat and add 2tbsp olive oil. Sauté onions for 2-3 minutes. Add garlic and continue to cook for another minute. Add spinach all at once and cook, stirring occasionally until spinach has completely wilted. Allow to cool slightly before proceeding.
To the spinach, stir in quinoa, parmesan cheese, dried herbs, lemon juice, salt, pepper and dried chili flakes. Set aside.
Rinse mushrooms and trim the bottom edge an approximate 1/4" and remove the stem down to the base. Using a spoon, scrape out the dark fanned bit, going down to the solid surface of the mushroom. Brush the outside of each mushroom with olive oil.
Fill mushrooms with an approximate heaping 1/3 cup of mixture, pressing just slightly to fill in the mushroom cavity. Top with tomato slices if desired and then sprinkle each with mozzarella cheese. Place filled mushrooms onto a parchment lined baking sheet and bake in preheated oven for 20 minutes. Turn oven to broil and broil for 1-3 minutes until cheese is melty and golden. Remove from oven and serve immediately.
Use 1/2 cup dry quinoa to 1 cup of vegetable or chicken broth and cook according to package directions. Yields about 1 1/4 cups.