Interesting point.
If Magus were to find Schala now since the Chrono Cross was used to free her, what would they do...
Perhaps travel back to prevent the Zeal disaster? If that were to happen and the Queen was put out of the picture, Zeal might exist today. It could be a museum or something else.
Then again, continents would be missing and a whole lot of gaps not filled that were filled before.
Dude, it's not just because of her mother, and Zeal can't just dissapear.
Also, I'm with Aura.
Firstly, Schala's power has almost come to a point of omnipotency. She can cross dimensions, think things that no human can and not age.
But yes, as Chrono'99 said, i'd hardly believe that they'd just settle down in the CC world, or let alone find eachother there.
I also saw as the final pages of the journal as another tribute to Magus, because it was smartly written to have no name, so it could very well be him.
Either way, Schala is going to find him in our world, either take him back to CC's world, or simply live with him in our world for a time (Like what Magus did with Kid in RD). That or after there'd be a reincarnation style sort of thing like what happened with the Frozen Flame, and heck, they may be reincarnated to be children of the reincarnation of Queen Zeal, who would be untainted.