Heat oven to 400°F (200°C) and line two baking sheets with parchment paper. Halve the spaghetti squash lengthwise, scoop out the seeds, and brush the cut sides with olive oil, salt, and pepper.
Place squash halves cut side down on a lined baking sheet and roast for 35 to 40 minutes, until the shell gives when pressed and a fork slides easily into the flesh.
While the squash roasts, combine ground chicken, panko, parmesan, egg, garlic, parsley, Italian seasoning, garlic powder, onion powder, salt, and pepper in a large bowl. Mix gently just until combined.
Scoop about 2 tablespoons of mixture per meatball and roll lightly between your palms. Arrange on the second lined baking sheet and brush tops with olive oil.
About 20 minutes into the squash roast, slide the meatball pan into the oven. Bake for 20 to 22 minutes, until golden and cooked through to 165°F (74°C).
While everything bakes, warm the marinara in a small saucepan over low heat or in a covered microwave-safe bowl. Stir in red pepper flakes if desired.
Let the squash cool for 5 minutes, then drag a fork lengthwise through the flesh to release long strands into a bowl. Blot gently with a paper towel if watery.
Divide squash strands among four bowls and top each with about five meatballs and a generous spoon of warm marinara. Finish with extra parmesan and fresh basil.