Your question forces me to restate the original post again in other words, but you're correct, if understanding and manipulating the substrate of our reality is

Your question forces me to restate the original post again in other words, but you're correct, if understanding and manipulating the substrate of our reality is a sign of "bad design". Nothing you mentioned is basic from the viewpoint of a mere single planet species. But it's all basic enough to ensure we've remained a single planet species. Thus, if you can build a Dyson sphere, you probably won't need one because at that point your fundamental knowledge will be much greater than "bigger gun". In fact, we stopped building bigger firearms long ago due to greater understanding.