[Update: and now there's a fifth discussion thread, which you should probably use in preference to this one. Later update: and a sixth -- in the discussion section, which is where these threads are living for now on. Also: tag for HP threads in the main section, and tag for HP threads in the discussion section.]
The third discussion thread is above 500 comments now, just like the others, so it's time for a new one. Predecessors: one, two, three. For anyone who's been on Mars and doesn't know what this is about: it's Eliezer's remarkable Harry Potter fanfic.
Spoiler warning and helpful suggestion (copied from those in the earlier threads):
Spoiler Warning: this thread contains unrot13'd spoilers for Harry Potter and the Methods of Rationality up to the current chapter and for the original Harry Potter series. Please continue to use rot13 for spoilers to other works of fiction, or if you have insider knowledge of future chapters of Harry Potter and the Methods of Rationality.
A suggestion: mention at the top of your comment which chapter you're commenting on, or what chapter you're up to, so that people can understand the context of your comment even after more chapters have been posted. This can also help people avoid reading spoilers for a new chapter before they realize that there is a new chapter.
A few thoughts, just to go on record with them. As always, apologies if I'm repeating well-covered ground; I have not read all the comments on this thread, nor am I likely to. I would appreciate pointers to comments I ought to read, though.
OTOH, the same person is described in ch52 as
It's unclear whose voice that is in, but the same sentence describes the voice as "unfamiliar," which suggests we're getting Harry's POV rather than Word Of God. So Harry believes Quirrell Polyjuiced into this man.
So either: A. Harry is right, and Bahry is mistaken about what's possible while Polyjuiced. B. Bahry is right, and Harry is mistaken about what happened. C. They're both right, and something weird is happening. (E.g., Harry's companion is not actually doing magic as delicate as he appears to be doing, or some such thing.)
B seems most plausible to me, as Bahry ought to know about such things. The simplest explanation is that he isn't Polyjuiced at all -- the "sallow lanky bearded man" with the "low and gravelly" voice is Harry's companion's natural form. (Of course, there might be other means of changing his appearance that we've never heard of before, but that would be a cheap narrative trick.)
Which suggests he is not and never was the actual Quirrell. And also that he is not and never was anyone Harry would recognize (from pictures, from extrapolation in mirrors, etc.)
So either: A. There is in fact no plausible reason for this. B. There is a plausible reason, but neither Quirrell nor Harry can think of one. C. There is a plausible reason, but Harry can't think of one, and Quirrell is pretending not to be able to think of one.
The most likely of those given the data I'm aware of is A. Which suggests that Professor Quirrell is not and never was possessed by Voldemort (ETA: er, I mean, by the shade of He-Who-Must-Not-Be-Named).
Which is not to say that Harry's companion isn't or wasn't.
The fact that Quirrel sometimes reverts to zombie mode suggests that Voldemort is teleoperating that body. Perhaps he has more than one body for that purpose, and simply used a different body for the breakin, rather than polyjuicing the first one. It would be odd that both bodies could assume snake-form, but I see no reason in principle why that magic wouldn't be transferrable.
If that's what happened, then the Quirrel body might still be alive somewhere. Voldemort might be alive (in which case he would return to Quirrel's body, and pin the blame on Harry), or temporarily dead, in which case Quirrel's vacant body might turn up somewhere.