If we make this the policy, what do we do when the subject of a piece does not provide that final round of comments? Do the subjects of articles get to prevent publication by withholding comment? Or can the articles go ahead without those comments?

Because what you're describing is generally what is done, what has been done for decades. This is why you often see a sentence near the end of an article stating that the subject declined to comment or did not respond when reached for comment.

The assumption seems to be that people are interested in truthful reporting. In fact, most subjects do not want truthful reporting. They want favorable reporting, which is often not the same thing.

There seems to be very clear evidence that Zimbardo lied, at least, and possibly acted extremely unethically, possibly even illegally. Why would he be interested in providing comments on a story stating so? What would be his motivation? By withholding his rebuttal until after original publication, he can base his response on which parts of the story are gaining traction, if any. In this case, he's doing just that, and ignoring several elements for which he has no good answer.

It would be very nice if life were documented in a series of objective wiki pages, but so long as humans are involved, that will never be practical.