I understand reticence in such a fantastic side-to-side team up, but at this point, I honestly don't see how it's not being set up with Cloud and Zack, in some form or fashion.
And if it's not being set up for that, what the hell is Zack there for?
From just weighing the possibilities, intentions, thematics, and alternatives, you have Zack being given a divergent second-chance in an adaptive remake that celebrates FFVII's 20 year history.
The writers state their intention of following the narrative arc of the OG while keeping FFVII fundamentally feeling like FFVII.
They intend to follow it's overall story.
An alternate timeline has been forked thanks to Zack being able to survive past his point of defeat.
Zack's uncovered something that's clearly off and more than likely serve as the launch point of something like a quest of his own.
I don't know how that doesn't lead to the same end point, which is Sephiroth. Who conveniently has been revealed to have a second alternate that appeared to confront Cloud at the end of Part 1 and alert him to the ultimate end of the planet in the far future, and vocalize his intention to forestall death by whatever means to continue his ambition.
Something's obviously being set up for a final confrontation that goes beyond what we know. No, it shouldn't overshadow the main plot, nor should it undo the core narrative themes. A final battle however is far more flexible as the final gameplay mechanic and capstone to an action RPG story. A new final confrontation can easily fit after the original final battle, and before the one-on-one against Sephiroth. There's far more space for it than something like, undoing the whole narrative entirely by doing something bizarre mid-game. If it's slipped on like a warp-around plot, it most neatly converges at the end of the story where these two things can finally intersect at the Edge of Creation. Just like we first got a glimpse of it in Part 1, it'd make sense to have it tied up at the very end. Zack may not literally be there for the final fight, but I can imagine it happening simultaneously, at the very least.
But something is going to happen. Zack's not just there for absolutely no reason or pay off.