I definitely think that this is a second worldline and the events that we have seen in Dark Road thus far are the rewritten ones. Honestly, I'd even go as far as to think that maybe the strange connection Xehanort has with Player may have something to do with this.
It's not only that intro sequence that is sketchy; the whole perception that their class has of outside worlds and how Xehanort arrived in Skaia in the first place is weird. They know Xehanort just showed up on the very same "pier" we know, but they don't know exactly how he came to be there, with some suggesting he came from the other side of the ocean, while Xehanort toys with the idea that he just fell from the sky.
Considering how he just goes through a Corridor of Darkness summoned by someone else instead of falling into darkness, one would think he would just show up on Skala perfectly fine, but it didn't seem like Xehanort was lying or hiding something when they were discussing that. So there's definitely more to this than just "time paradox lol" and something probably happened with him when he arrived in Skala, or even before that.