Preheat the oven to 425˚F (218˚C). In a small bowl, combined TVP and stock together and set aside to hydrate. Place cut and seeded spaghetti squash on a parchment lined baking sheet.
Drizzle about 1 tablespoon olive oil over each half of squash and brush with a pastry brush to evenly coat. Add 2 whole garlic cloves to the inside of the squash. Sprinkle evenly with ½ teaspoon oregano, and all the salt, black pepper, and red pepper flakes. Add more or less spices to taste. Place cut side down (with garlic cloves underneath). Bake for 40-50 minutes. The edges should begin to become caramelized.
To a blender or food processor, add tomatoes, hot sauce, remaining 1 teaspoon oregano, smoked paprika, fennel, seeds, and onion powder. Pulse till combined and the sauce is slightly chunky, about 1 minute.*
Over medium heat, add remaining 2 tablespoon oil to a large skillet. Add onions and peppers. Saute for 3-5 minutes or until softened. Add hydrated TVP, stir together, and cook for 3-5 more minutes. Add blended tomato sauce and stir together. Allow to continue to cook until heated through. Stir in pesto and fresh basil. Remove from heat.
Once squash has been removed from oven, allow to cool for 5-7 minutes. Flip flesh side up and carefully use a fork to smash the softened garlic cloves into the squash. Use a fork to pull the squash away from the skin and resemble a pasta like texture. Fill with the sauce mixture. If using, sprinkle non-dairy cheese evenly over the squash and return to oven until broil until melted, careful not to burn. Garnish with more fresh basil if desired.