So I have just defeated the Pontiff in the English 2.05 version (second playthrough, first was in the original Jap version) and I notice a difference that I am not sure if I remember right -- the Pontiff in my first playthrough combined with both the Stoic and Shy girl, with all of them dying in the end and then absorbed by the black slime; but now in this playthrough there has been an additional cutscene (can't remember if it was there in the first playthrough) where the Pontiff's Devil stabs him and he pushes aside both the Stoic and Shy girls, ultimately leaving them alive at the end of the fight.
I haven't progressed at all after the fight so I am not sure if the two can be saved or not but I felt like sharing this in case nobody else noticed the difference. What I did in this playthrough is just get all of the scenes, hidden items, and additional quests that I could (level is currently mid-60s).
Edit: The Black Slime showed up and only absorbed the bloody remains of the Pontiff - both girls are still alive.
Edit 2: Both Stoic and Shy girl chill out after Pontiff's fight in the lab room with the huge fly in it. Both of them have no dialogue yet and are quiet (my interpretation is that they are there so they can follow the last Pontiff which is in the form of the massive fly. This is pre-blue sorcerer.
Edit 3: I have defeated Blue Sorcerer (spare route) and they are still there, chilling. There is a soft bug in which if you go in the room where you fought Fused Pontiff both girls are left there crouching and silent. I am not sure what to do with them, I have tried everything - going there at night, wearing the Holy Garments (in case they wanna have a scene with new Pontiff), looking at the family photo in the hidden room again (either the people in the photo references them or the Pontiff's family, hence the whole"I have nowhere to return to"). If anyone finds what you can do with them, then please share, I have done about every side-quest that you can without a guide.
Also, the number of girls you can have a scene with are 47 (counting the Slave Girl if you choose not to save her at the hideout, I have not done that) at the moment (Evil's passive skill counter) - did anyone get a higher value?