Part 6 Questions and Implications

It seems pretty obvious to me that Pucci wins. He activates Made in Heaven 2 times, and everyone that was alive now has to go through life knowing their entire fate

This is where you're wrong and probably why you're confused, Pucci didn't win because he wasn't able to achieve his ultimate goal, create a universe where everyone already knows their fate, he had to stop the acceleration of time against Emporio and ultimately got killed by him, which caused the reset of the universe where Emporio fought Pucci in the Ghost Room, and created the alternate timeline where Jolyne is named "Irene" where everyone is still alive but don't share the same fate as their alternate versions.

/r/StardustCrusaders Thread