Now that people will stop making jokes about Nia and Melia together, Melia is gonna get left out again. So what is the state of the queens at the end of this? Gone? Has the system been revised?
You know if this world keeps on going and the pod system somehow remains, my crackpot theory of the day is that Melia continues to exist, and the world eventually regresses to the state of Mira in X. And the Endbringer Telethia from X will turn out to be Melia. I am really hoping Melia doesn't get it this bad, but the trajectory isn't looking too good.
I think you're reading too much X into this. This technology has been a major part of almost every Xeno game since Xenogears. X was trying to be different by making them robots instead of biotech. The biotech existed in X but it was extremely limited to be used as a final process after settling a planet and was treated as a major moral dilemma for the people of Earth.
Xenogears: Kadomony is a computer that can create organic life. The Zohar creates Elly using Kadomony and most of the planet is populated by people desended from people created by Kadomony after most humans perished in the crash.
Xenosaga: Realians are artificial humans created with a similar technology.
Xenoblade X: The Lifehold was a computer housing DNA material to recreate the bodies of everyone stored in its memory banks.
Xenoblade 2: Blades are artifificial lifeforms created with a similar technology.
Xenoblade 3: Everyone are basically Blades.