My interpretation of this is that Square are making clear that this is not going to be a 1:1 remake from now on. And lets be honest, it wasn't 1:1 anyway, it's just that any time important events started to play out in a slightly different way, the whispers would come and correct it.

The visual clues in the end show us that Zack surviving his death in Crisis Core is not in the same timeline as the story we're following. So I firmly believe that he, along with Biggs, Wedge and Jessie are deceased in our story, just like in the OG. But even if 'our' past did change so he survived the Crisis Core ending... the final shot we have of Zack is him carrying Cloud towards the edge of a a cliff overlooking Midgar... which, in the original game is exactly the situation where he was killed. So whichever way you look at it, thinking he's alive and kicking somewhere is not a sure bet at all.

So I really don't think they're trying to mess with events in the story that have already taken place. The whole plot with the whispers is, in my view, more a statement of intent. A way of showing us that things may change going forward, some small some big. Obviously the big one is Aerith's death, and what they've done does open up the possibility that they let her live. I feel fairly confident that the fundamental, critical aspects of the FFVII story will be left in-tact, but the way we hit those plot points may change significantly.

Look at the Honey Bee in sequence, that was a really big deal to include. OK, it's not plot-critical like Aerith summoning Holy is, but it's an example of how there was an important objective to accomplish: 'Put Cloud in a dress.' But the way they did that was completely different to the original. The road to get there featured 4 new characters, a coliseum and a Honey Bee in vastly changed from its original form. And yet, it did exactly what it needed to do. The journey may have been different, but Cloud ended up in a dress and I have yet to hear a single fan of the original complain about it.

This is the kind of approach I'm expecting going forward. The Unknown Journey Will Continue​ - the Journey will be very different than we remember, but we'll still end up at the key destinations along the way.