Preheat the oven to 350 degrees. Spray a 9x13-inch baking dish with cooking spray.
Bring a large pot of salted water to a boil. Add the pasta and cook 1-2 minutes short of the cooking directions. Drain, saving some of the pasta cooking water.
Heat olive oil in a large skillet over medium-high heat. Add the onion and cook, stirring occasionally until translucent, about 5 minutes. Add the garlic and cook, stirring, for 30 seconds. Crumble in the plant-based meat substitute and cook until browned, about 5 minutes. Add the beans, tomato sauce, diced tomatoes, chili powder, garlic and onion powders, 1 teaspoon salt, and pepper. Cook uncovered for 10 minutes. Add the pasta and queso and stir to combine. Thin with some of the reserved pasta water if it is too thick. Pour into the prepared baking dish and bake for 20-25 minutes.