My interpretation of that was extremely different: that Harry got riddled when he was a baby, in Godric's Hollow.

In canon, Ginny reads the diary a lot and this enables Riddle to take her over when he wants to. When he does, she's basically a puppet: it's (fully aware) Riddle scrawling on walls and summoning basilisks, and Ginny's completely unaware of it; afterwards, Ginny is basically her normal self again, with no memory of what Riddle did while operating her body.

There's no sign in HPMOR of anything like that happening to Harry. The Harry whom QQ addresses as "Tom Riddle" has (so far as we can tell) psychological continuity with the Harry we've been following through the previous hundred-plus chapters. There's no sign of "absences" like Ginny had. After being addressed as "Tom Riddle" (and, again, with no indication of any personality changes or anything) Harry resolves explicitly that he is going to do whatever he can to stop QQ. So if we are supposed to understand that the diary had some major effect on Harry, it has to have done it in a way that doesn't "mirror canon" much at all.

What I think is being described here is something more like a personality-upload from Voldemort to baby-Harry, so that what remained in Godric's Hollow that day was (at least according to Voldemort's plans) Tom Riddle implanted in baby-Harry.

(What I can't work out is whether we're supposed to understand that it went wrong, with the Riddle personality getting kinda isolated, like grit in a pearl, as Harry's "dark side", or that it worked exactly as planned and the Harry we see now is what you get when Tom Riddle's mind grows up in baby-Harry's brain, raised by his adoptive parents. I'm not even sure what the latter means exactly. Perhaps the idea is something like this: after the upload, what we get is more or less the same as what we'd have got if baby-Riddle had been raised in Harry's place, but Riddle's adult memories are also stashed away for later use and the latter are the "dark side".)

[EDITED several hours after posting to fix an embarrassing word-omission. I don't think the sense was ever unclear.]