Y'shtola COULDN'T leave the Lifestream. Emet-Selch COULD, while alive, due to the fact that he was an Ancient and connected with the Lifestream. No one is denying that.
The jump you're making is that Emet is able to LEAVE the Lifestream after having been killed. You directly said he's not dead, and that he CHOOSES not to come back. When living things die in FFXIV, their aether is redistributed into the flow of the Lifestream - They become part of the river, effectively. This is very different than riding the Lifestream as Y'shtola and Emet-Selch did - Y'shtola FORCED herself into the Lifestream, and had no way to escape. She would have been entirely consumed by it and redistributed amongst it's flow, were it not for the elementals/Emet-Selch yanking her out before that happened.
As for Emet-Selch, I would not be surprised if there is some Ancient magic that allows him to ride the Lifestream unperturbed, or if it has something to do with his soul being entirely unsundered while alive. Nontheless, when he died, his aether too dispersed - To be reaborbed by the flow. He has no power over the Lifestream in that state. He's gone - Just aether, like all other dead beings.
.[/B]