Cornucopia Machines can't transmute elements, they only do chemical alterations, and maybe sort nuclear isotopes. If you want to make an iron axe-head with a CM, you'll need to feed it the right mass of iron. No Iron? The machine is smart enough to try to find other elements which can perform similarly, but you can't make an iron axe. This gets extra critical when elements are not easily substituted, like in nuclear batteries, fission reactors, sensors, or high-performance alloys. Mining elements is still a critical industry solar system wide. Much of the inner system is rich in heavier elements like metals and fissionables. Conversely, the outer system and parts of the asteroid belt are much richer in light gasses (important for fusion) and many volatile compounds. Most processing is likely done with a nanofabricator or recycler rather than older macroscopic processing, but it still needs to be done to make feedstock.