The whole "Building the world" similar to Legend of Mana is actually a bit of Gameplay and Story Integration if you think about it - since technically, Marche and his friends created the world using the grimoire, that's actually Marche imagining where things would be. (Although some like the palace and Ambervale are in pre-determined locations)
Because Marche didn't place them; Mewt did.
Some people laugh at Marche, Ritz, and Mewt for having such silly wishes...but consider that they're at least twelve years old. Twelve-year-old kids are of course going to do stuff like wish for their hair to be naturally red so bullies won't bother them, for their dead mothers to be back in the family again, and for their bullies to meet cold deaths in the snow. Of course they won't think of the consequences of their actions - they're little kids.
Likewise, Doned's actions are going to make a bit of sense when you consider he wanted to walk and run like other kids...and if you interpret Marche as a Villain Protagonist, he thinks Marche is going to destroy it all for him.
In an early mission, you save a professor from three 'lost ones,' the animated corpses of people that are lost in the snow. Their names? Colin, Lyle, and Guinness, the three bullies from St. Ivalice. You then proceed to kill/exorcise them. Later on, you fight them again, this time as vampires.note You do see the three bullies at the end of the game, so they were apparently restored when the rest of Ivalice faded away. But there's more fridge horror. Do they remember?
Even worse is the fact that everyone in Ivalice is someone from the real world with another personalty forced onto them and the kids are rather okay with it.
What about the fans who are OK with it and insist that Marche is evil for restoring things to the way they were?
Marche had no idea exactly how things worked. He knew some people got carried over but not that everyone else did too. Babus even tells him he has memories and experiences of his whole life. Replaced people or not they're still full people with full histories. Yes he wants to restore the old world, but it's not until the last moments he does so in any way other than completely destroying the current, existing, and very real one.