Several speculations/thoughts/questions:

First, did baby!Harry actually in fact survive the killing curse? ie, perhaps the curse successfully detached baby-Harry's-soul (presuming that something like "souls" exist in MoR... given the presence of Horcruxes, I'll tentatively assume yes), but the body was immediately made into a Horcrux... so Voldemort-soul-shard effectively inhabited that body. Essentially Rationalist!Harry is actually more like what Voldemort would have been like if raised in a loving and sci-fi and science loving family.

The Hat did say that if there was bits of the Dark Lord's mind there in addition to Harry, it would have noticed the extra "passenger"... But in this case there really is only one mind/soul/whatever. The catch is that mini-mort is all that's there.

This brings up the possibility of if this was an accident or deliberate. Perhaps Voldemort actually deliberately planned/faked his apparent "death"?

(Possible related, well, possibility: How do "we"/they actually know Voldemort even used the Killing Curse that night, as opposed to doing some other thing? ie, how is it known that he is the Boy Who Survived the Killing Curse in the first place?)

Further speculation: When Quirrellmort was lecturing in class about how he used to want to be a Dark Lord, but now finds that he really just wants to teach how to fight and such... perhaps that's a literal statement of fact? ie, does he even desire to "rise again as the Dark Lord Voldemort", or is this what he actually wants now?

Further further thoughts: Does Dumbledore know that Quirrell is really Voldemort under-the-hood? Not just knowing "there's something odd here", but actually really knowing that as fact?