For anyone who might still be confused, no, the ‘Multiverse’ is NOT back. The Dark Aether still has remnants of it, but those universes are permanently gone. We still only have the 2 main universes: the ‘perfect’ universe and the Dark Aether.

The dark Aether is HUGE and, essentially, every reality from the old story was thrown into it haphazardly by Nikolai. Places, people, and powers all got jumbled together into a cohesive mess.

This would explain why these things still exist and are leaking into the perfect universe; they didn't get erased or reset. They are just somewhere in the dark Aether. It also explains why our 'original' crew is back, but from different realities. As to how they kept their sanity all these years, it is yet to be explained.

This is more theory territory, but I believe all the Sentential Artifact did to the BO6 crew was swap their 'dimensional frequency' with Richtofen's dead family/S.A.M's new body. Similar to what Panos did to the Liberty Falls strike team. Now the fabric of reality believes that the BO6 crew 'belongs' in the dark Aether.

As to why the BO6 crew is fully in the dark Aether and not 'halfway' in like Panos was, or how the strike team is now, I'm not sure. I believe it's because Panos was still alive when they swapped, and for S.A.M./Richtofen, what they needed was to essentially resurrect the dead, thus requiring more life force out of the BO6 crew.