This is an interest observation, and seems true for future versions of AI, but when the current technology is based on human language, I don't think I would make the assumption that LLMs would directly translate to manipulating machine language.
While it is true language is an important input, there are plenty of examples of transformer architecture working on generating binary data - a good example would be generating a 3d mesh from a text prompt (you have a shit ton of models for this). The input is text, the output is a binary file - a jpeg, a png or an stl. We're already there, just not for applications.
Fyi you can do this today. Ask for a flying cape dog and have a stl you can print into a physical object.