I think the main limitation on the current models is not that cpu instructions aren't cpu instructions (even though they can be with .asm), it's that they are causal, the cpu would need to generate a binary entirely from start to finish sequentially.
If we learned something over the last 50 years of programming is that that's hard and that's why we invented programming languages? Why would it be simpler to just generate the machine code, sure maybe an LLM to application can exist, but my money is in that there will be a whole toolchain in the middle, and it will probably be the same old toolchain that we are using currently, an OS, probably Linux.
Isn't it more common that stuff builds on the existing infra instead of a super duper revolution that doesn't use the previous tech stack? It's much easier to add onto rather than start from scratch.