We might not know the "real" Yda, or everything about Yda, or even nearly as much about Yda as Papalymo knows about Yda, but I doubt that the Yda we know is a ringer for the "real" Yda. Everyone got changed somehow for their experiences in the Lifestream. Y'shtola, Thancred, they're not quite the same person they were prior to that experience. So expecting Yda (and Papalymo) to act exactly the same way they did prior to the Lifestream does not work.

And remember, all of the Scions accept that Yda is Yda. They have been fooled before (as recently as the events leading up to the main fight in 3.4) but I doubt that we are being fed another "Scions are deceived!" thing again, not quite so soon anyway.