Basically, yes.
Slightly pedantic answer: they're still different people, but Voldemort appears to be possessing Quirrell, through some means different than the means used in canon, so that it isn't too easy for Harry to figure out what's going on.
Fully nuanced answer: referring to the villain as "Voldemort" may be misleading, because in this version it appears the person who was born Tom Riddle has gone through all kinds of identities and personas and the "Voldemort" persona seems to be less important to him than in canon. Also, though I consider it unlikely, I'm not sure we can entirely ignore the possibility that Riddle magically forked himself, and there are multiple spirits descended from Riddle running around. Also, for all we know the original Quirrell could be flat-out dead, and Riddle (or this particular spirit descended from Riddle) grabbed the body of a random muggle to use while impersonating Quirrell (again, may not be terribly likely).
It's also possible that Voldemort/Quirrell isn't Riddle.
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: