Obviosuly Zack comes from a different timeline, and we see that in the origianl ending, but I think the "new" ending heavily heavily implies he's in the real timeline. It doesn't offer a sinle clue that it's not the main timeline.It doesn't suggest it anymore than the original ending did.
The stamp packaging is the biggest hint that it's not the same timeline. There's been nothing contradicting it as a different timeline since that.