In a 12" skillet over medium high heat, add the olive oil, onion and red pepper. Reduce the heat to medium and sauté just until the onion softens a bit.
While you wait for the onions to soften, scoop just a bit of each zucchini out with a round scoop (or use a round measuring spoon). Chop the scooped bits up into a small dice put the zucchini aside.
Add the tomato, zucchini bits, thyme leaves and some salt and pepper to the pan. Continue to sauté for another couple of minutes. Add the spinach and stir until the spinach wilts down.
Remove the pan from the heat and add the cooked quinoa and sprinkle with some fresh basil leaves. Add the Parmesan if using. Stir to combine and set aside.
Preheat your oven to 375 degrees.
Line a baking sheet with foil or parchment for easy clean up. Arrange the zucchini on the sheet. Using a small spoon (I use a regular teaspoon) divide the mixture between all of the zucchini. Cover the baking sheet with foil. You can refrigerate at this point up to a couple of days if you'd like to serve it later. Otherwise, place the sheet in the oven and bake for 30 minutes, covered.
After 30 minutes, uncover and top each zucchini with some mozzarella. Place the sheet back in the oven and bake for another 10 minutes. If you'd like a browner top, raise the rack in the oven to the highest spot.
Remove from the oven and serve.