So, this is the single change that makes this story an AU?

I was thinking along those lines as well, but at that point in time Voldemort was already significantly different from canon.

There seem to be much more changes, even that is probably the most important one.

Time Turners don't work the same (in canon, there is no hard limit on 6 hours, it just becomes exponentially dangerous if you try that), the Sirius Black/Pettigrew thing doesn't turn out the same at all, the Free Transfiguration stuff doesn't seem to work the same, ...

And as others mentioned, Voldemort is much more competent.

Right at the front of the whole fic he says this isn't SPoD.

As a point of interest, wasn't it Merlin's original intent that, at minimum, everyone mentioned in a prophecy should have access to it? It was only centuries later that the Unspeakables sealed the prophecy records away, so why does the Line of Merlin Unbroken have a function for bypassing that seal, how does anyone know this, and why is using it forbidden?

Well, that and the differences in the setting/magic (there's no Free Transfiguration in canon, for instance, and the Mirror is different - there are less Mysterious Ancient Artefacts generally - and Horcruxes run on different mechanics ... stuff like that.)

And Voldemort is just inherently smarter than everyone else, too, for no in-story reason I can discern; he just is, it's part of the conceit. (Although maybe that was Albus' fault too, somehow?)

So, this is the single change that makes this story an AU?

From chapter 1:

This is not a strict single-point-of-departure fic - There exists a primary point of departure, at some point in the past, but also other alterations. The best term I've heard for this fic is "parallel universe."