I'm pretty sure the post Yaldabaoth
section of the game where Ren is Not in Juvie
and all the other stuff is happening is a dream sequence. It explains the random things that seem to happen like Okumura and Wakaba
not being dead. Maybe a Lotus Eater Machine type thing done by some big bad as the final boss of this new scenario.
Also, Okumura is upset because he has to be in a place with so much poor people.
(edited by Gin)