Preheat oven to 425°F.
Cut 1/2 inch from the pointy end of each squash, then halve each through it's center. Spoon out and discard seeds. Rub squash with 1 Tbsp oil and season with salt and pepper to taste. Arrange on baking sheet and roast, hollow sides down, until tender, about 25-30 minutes.
Meanwhile, heat remaining 2 Tbsp oil in a large skillet on medium. Add onion, season with salt and pepper, and cook, covered stirring occasionally, 8 minutes.
Uncover and cook about 6-8 minutes more, stirring occasionally until onion is very tender and beginning to turn golden brown. Stir in garlic and thyme and cook 2 minutes. Remove from heat.
Place cauliflower rice in a microwave safe dish. Heat until warmed completely through. Place spinach on top of the rice and cover with a lid. Let stand 5 minutes.
Transfer squash to a platter or individual plates, hollow sides up. Fold spinach and green onions into rice along with onion mixture, then spoon into squash halves to serve.