They're probably using the same thing the rest of the internet is using to suggest its a different timeline, the Shinra dog mascot in the Zack sequence is shown to be a different dog to the one used throughout the rest of the game.
There are 18 chapters total. You can also complete battle intels in chapter 16 one part of the shinra building. One battle intel requires you to master all 12 green magic materia so if your not using all of them remember to swap them around.
If you use Tifa's unbridled strength to upgrade...
I think the girl who lives in Elrichs old house, who goes to Stanford stole it. Thats why she bailed out hard when talking about her project and then finding out who they were.