That's rhe most air tight part, Midgar itself was displaced, but not the planet. The only things that would have a second timeline equivalent would he outside of Midgar, so Jessie would be at the gold saucer, but if she survived and was still in Midgar by the end, there would be two jessies.
There wouldn't be more then one of any of the main cast (EXCEPT MAYBE CLOUD, DUN DUN DAA!) because they were either always in Midgar during the events of FFVII Remake, or were always outside of it. Tifa and Barret and Red XIII and Aerith never left Midgar during the time between Zack arriving (which I mark as the point the Midgar was displaced, roughly a month or two before FFVII starts or something) and the end of Remake.
And everyone outside of midgar, like Yuffie, Vincent, and Cid, weren't in there during that time anyway, so there isn't a reason for them to be displaced, not to mention they literally have just been living their life at the time so like, nothing should change with them anyway.
Cait Sith is a different story, but suffice to say they aren't an issue either.
I can only assume, for really cool story purposes, that Midger was actually, Literally displaced to right after Zack's last stand, as the ending implies through the shared experience of the glittery rain both in midgar and with zack, framed to be happening at the same time.
So while Zack carrying Cloud didn't literally pass Aerith and Cloud in the ending, they Figuratively and Practically did.
Zack went home and plyed his new trade as a Merc for hire with Avalanche as Cloud was left to recover with Tifa, and went on basically the same missions and adventures as Cloud did on FFVII, only as a happy-go-lucky guy with massively more power and training then Cloud's moody patootie.
This basically went the same way though, with the exception that Zack literally had positive connections with some of ShinRa's employees like the Turks, and would have left Midgar on affable terms, or at least would have had a... different reaction to the Plate Drop situation, I'm fuzzy on how that would go. Probably would make zack a bit PO'd : P
Anyway, bottom line here, I'm messing up a lot of my original theory here, but the point is, Cloud would recover a lot better and Zack would basically be taking the place of cloud in the story, only with his Crisis Core Loose ends making up a deviation from FFVII's plot, making him leave Midgar early and set out to find Sephiroth himself while taking cloud with him, and leaving Aerith for her safety (or maybe sue comes with, I dunno, there are holes in this for sure).
SO, BOTTOM LINE, there are probably gonna be a Cloud and a Zack from the new timeline doing stuff ahead of the party, and either new cloud or old cloud (old cloud having muscle memory of the last timeline through sephiroth's connection, more subversed then Aerith's actual legit knowledge of what happened in FFVII) are gonna be a pawn of sephiroth to maintain the bringing of Reunion so he can snag Meteor without his shit getting messed up this time.