I don't think we're necessarily in disagreement here: I agree that determinism should be taken as far as possible, but once we zoom out of the software engineering world I think things tend to get a lot less easy to automate if that makes sense.
As coding agents have accelerated my work, I just build tons of tooling around existing software. Or in rare cases build new ones. If we zoom out of software engineering, we will still be in the realm of files - text or binary. That does not change.
The question is - do we let agents run the tools or the "programs" call the LLMs. The OS is the new agent, but not the same sense of "agent". I want LLMs to be lightly sprinkled in a future "agent" OS, not the other way around.