I can't believe I didn't realize this before.

Someone complained elsewhere (I think it was in the other thread) about Harry being the Boy-who-Lived and having a prophecy and having a cold dark side and being super-rational.

From MoR itself:

It's too much coincidence for one girl to be the strongest magically and academically unless there's a single cause.

It's plausible that one of the Muggle-raised students at Hogwarts could be a science nerd. It's not plausible that that student would also be the Boy-who-Lived. There must be a single cause.

I think it's most likely that Harry's dark side is somehow an effect of being AKed. Perhaps he's a horcrux, like in canon. The hat said no, but it's possible that Harry was killed and the only soul left in him is Voldemort's fragment. Or, without positing souls, maybe horcruxing a person overwrites the victim with a copy of yourself.

Harrymort has a warm side because he was raised in a loving household; he doesn't remember being Voldemort because he was stuck in a child's brain, with the plasticity and pruning that entails (or maybe V. wiped Harrymort's memory for some reason?); he didn't survive the attack, but rather his fresh corpse was appropriated as a horcrux.

This also explains his prodigious intellect and indignation at being treated as a child: he's really an adult mind, overwritten onto a child's brain. This is also why the Remembrall reacted the way it did: he's forgotten decades of his former life as Voldemort.