Preheat your oven to 375°F (190°C).
Prepare the Cue Ball Squashes: Carefully cut off the tops of the cue ball squashes to create lids. Scoop out the seeds and some of the flesh to create a hollow cavity. Set the lids aside.
Coat the Cue Ball Squash - Rub olive oil, sea salt, and freshly ground pepper completely coating each squash.
Arrange in a Baking Pan - Arrange each cue ball squash evening in a baking pan. Be sure the squash aren't touching each other as they'll need room to cook all the way through.
Place in the oven for 20 minutes.
Prepare the Stuffing: In a skillet over medium heat, add a drizzle of olive oil. Sauté the diced onions until they turn translucent and fragrant, about 2-3 minutes. Add the diced bell peppers and zucchini, and cook for another 3-4 minutes until they soften slightly. If using, add the cooked and crumbled ground turkey or tofu and cook for an additional 2 minutes.
Add Seasonings: Sprinkle in the chopped thyme, red pepper flakes, salt, and black pepper. Stir to combine, allowing the flavors to meld.
Remove the Squash from the Oven - Your cue ball squash should be well-cooked, but not too soft or mushy. Allow them to cool.
Spoon In the Stuffing - Using a serving spoon or ice cream scoop, spoon in the rice stuffing. Cover with the baked top and secure with toothpicks.
At this point, you can put the stuffed cue ball squash back in the oven and bake for 5-10 minutes, However, it's not neccesary since they squash and rice stuffing are already cooked.
Cool and serve!