Cut the stem away from the broccoli and break up the florets into bite-sized pieces. Peel the tough outer layer of the broccoli stems, revealing the tender inner stalk. Roughly chop the stems and keep them separate from the florets.
Heat a large sauté pan over medium heat. Pour in 1 tablespoon of olive oil and swirl it around. Add the chopped broccoli stems and season them with sea salt and black pepper. Sauté the stems until they turn bright green, about 5 minutes. Then, pour in a splash of water and close a lid on top. Continue cooking until tender, about 3 more minutes. Transfer the sautéed stems to an upright blender.
Return the sauté pan to the stove over medium heat. Pour in the remaining 1 tablespoon of olive oil. Add the shallot to the pan and sauté until soft, about 2-3 minutes. Then, add the broccoli florets to the pan and season with sea salt and black pepper. Add the garlic and chili flakes to the pan and stir until fragrant, about 30 seconds. Pour in a big splash of water and place a lid on top. Cook until the broccoli is just starting to get tender, about 6 minutes. Then, turn off the heat.
Transfer half of the sautéed broccoli mixture to the blender. Keep the remaining sautéed broccoli in the pan. Into the blender, also add the cashews, nutritional yeast, miso, lemon zest, lemon juice, and basil. Blend the mixture on high until completely smooth. Pour this thick sauce back into the sauté pan.
Cook your short pasta according to package directions in well-salted water. Before draining, reserve about 1 cup of pasta cooking water. Once the pasta is drained, add it to the sauté pan with the sauce along with the reserved sautéed broccoli mixture. Stir it all together to combine. Add reserved pasta water until you have a creamy and fluid consistency. Serve immediately with extra basil, drizzles of chili oil, and extra black pepper on top.