I think you're vastly overestimating both the leverage a low-level employee would have in one of those megacorps and the amount of autonomy that an HR rep would have in a case like this. They have a process to follow, and that process does not include negotiation. Maybe they have the power to escalate the request to someone with decision making power, but that's going to take time, and their flowchart probably does not allow for allowing somebody to start work provisionally until that escalation is solved.

What "legal repercussions" are you thinking of? The author stated that their new contract was "at will", so their employment could be terminated for any reason at all.

(Not defending Amazon here. But the employee had been put into a position where they had no realistic choice but to sign.)