@zombiepie: Blasphemous is not literally capital C branded Christianity, so if that counts, they only need to be a pope-like figure. This list is really only limited by what I know about off the top of my head.
If that is the case I would like to recommend Zera Innocentius from Grandia II.
Now does the final boss have to be a literal pope or can the final boss be a metaphorical Pope? For example, there are a lot of JRPGs that have evil Pope-like figures as final bosses, but the Pope-like figure is not literally the Pope of The Latin Church.
@zombiepie: Well if rumors are to be believed, you may be in luck! Supposedly they are indeed working on a new Armored Core game, might be the next game they release before the inevitable Elden Ring 2.
I know you preface this list by saying "modern" From Software titles, but this list is reminding me of how much I wish they did ANYTHING with the Armored Core IP.
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