I have to depart from the majority of responses to your question and offer, "There is yet insufficient data to answer the question."
The tendency is to answer a qualified "yes" because that would be the answer in regard to canon. However, this is not canon. It also isn't an alternate history of canon, since Eliezer has modified things where he felt it made more sense to have them changed. For example, there is in this post a comment by Eliezer stating that he places the Peverells before the founding of Hogwarts, whereas canon states that Hogwarts was founded first (the decision makes sense, considering that Hogwarts itself seems to offer enough continuity of knowledge to make strange the idea that the Peverell story could have been reduced to myth given that their artifacts actually exist).
In short, the only reason people are so sure that Quirrel is Voldemort is because he was Voldemort in canon.
I don't think there is very strong evidence for it, but there isn't really sufficient evidence against the hypothesis either. Canon!Quirrel and HPMOR!Quirrel don't even appear to represent the same character (they use the same name, but there the differences basically stop, and the HPMOR version appears to be a case of identity theft). So in that sense, not only is what we know from canon unreliable, but we're not even really talking about a character that is derivative of his counterpart in canon, so all bets are off.
What people might point to as evidence (the zombie state, the feeling of dread, and the danger of Harry and Quirrel casting spells on each other) are things that invoke enough similarity to canon to encourage people to think of them as evidence that the situations are identical, but those pieces of evidence are fundamentally different between canon and HPMOR.
In canon, Quirrel usually acts rather normal with no hint of a zombie state and actually isn't even possessed when Harry sees him in the Leaky Cauldron (he seems to give Harry the dread feeling in that scene in HPMOR)-- because we know in retrospect that he was possessed for most of the book, we have a tendency to incorrectly match that with the zombie state in HPMOR.
In canon, Harry's scar physically hurts when Quirrel turns away from him while he's possessed. In HPMOR there is the the 'feeling of dread,' which isn't reliant on Quirrel's orientation to Harry at all, but rather it is reliant on proximity and the state of Quirrel's mind (it is reduced in both Quirrel's zombie state and in his animagus form).
In canon, the resonance between Harry and Voldemort is between their wands, not between themselves (Voldemort is able to cast torture spells on Harry just fine). The encounter between Harry's Patronus and Quirrel's Avada Kedavra did not create a Priori Incantatum event in HPMOR. It also affected Quirrel rather more severely than it did Harry.
From this, one has to conclude that this evidence that Quirrel is Voldemort is inconclusive at best and is generally misleading. It doesn't discount the possibility that HPMOR!Quirrel is possessed by Voldemort in a way that results in somewhat different symptoms, and it doesn't discount the possibility that Quirrel is actually Tom Riddle in the physical and mental sense.
So, insufficient data to answer the question. But add in author agency and you have to really question the obvious solution that we're being led to by things that only seem similar to canon. And I should note that "author agency" may also freely apply to comments the author has made outside the story as himself.
What people might point to as evidence (the zombie state, the feeling of dread, and the danger of Harry and Quirrel casting spells on each other) are things that invoke enough similarity to canon to encourage people to think of them as evidence that the situations are identical, but those pieces of evidence are fundamentally different between canon and HPMOR.
These aren't actually things I would point to as evidence of Quirrell's identity (though they are certainly suggestive of.. something). The Pioneer plaque thing may be one, but here are some clues t...
This is a new thread to discuss Eliezer Yudkowsky’s Harry Potter and the Methods of Rationality and anything related to it. This thread is intended for discussing chapter 96. The previous thread is at almost 300 comments.
There is now a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author’s Notes. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system.
Also: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, .
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: