I also am trying the NG+ in Midnight Mode in I cannot trigger the first purification/assimilation scene no matter which version I do, since after activating the pile drivers or removing them, the pad to begin the sequence does not appear. Also when this happens, the coffin recall system does not trigger. Even after going back a while with another save file the glitch still triggers.
Edit: This is intended nvm. Midnight sets LD to 0 so the only way to start these sequences is with rain men, we are good now.