Preheat the oven to 400°F (200°C).
Brush a thin layer of olive oil on the cut sides of the spaghetti squash and season with garlic powder, sea salt, and cracked pepper.
Place the squash halves cut side up on a baking sheet and roast until tender, about 30 minutes.
While the squash bakes, combine the softened cream cheese and 2–3 tablespoons pesto in a bowl until smooth.
Stir the chopped spinach, shredded parmesan, and 1/4 cup shredded mozzarella into the cream cheese mixture; add more cream cheese if too thick and season with crushed red pepper to taste.
When the squash is done, let it cool a few minutes, then use a fork to scrape the strands from the flesh into the halves, leaving them in the shells.
Divide the creamy pesto-spinach mixture between the two squash halves and stir it into the spaghetti-like strands until combined and fluffy.
Top each filled half with the remaining shredded mozzarella and return to the oven for about 10 minutes, or until the cheese melts.
Remove from oven, sprinkle additional crushed red pepper if desired, and serve hot.