To anyone struggling to get the last few entries, check your Logbook and watch a complete 100 Logbook guide on YouTube. That way you know exactly what entries you are missing. Then, check the guide below and you should be able to find out where to find some of the missables or hard to find lore entries.

https://psnprofiles.com/guide/17783-fatesamurai-remnant-trophy-guide#48-the-all-knowing

i have all characters in biographies but the porcentage still in 97%

I GOT THE 100% LOGBOOK TROPHY ON PS4/PS5 AFTER Update 1.0.3. The 88% for digressions is a SEPARATE tally. Logbook just covers profiles, locations, terminology and anything in the 3 categories. NOT DIGRESSIONS. DOES NOT REQUIRE ANY DLC.

Gongenyama Castle logbook entry was the final one I needed. For anyone who needs it clear on how to get the Gongenyama Castle logbook entry. READ THIS:

Meet/fight Rogue Archer in Kanagawa port. After beating him finish the Spirit Conflict and head for Tamanawa. Then HEAD HOME. The following day you can return to Kanagawa Port during the day. You'll start on the bridge. Enter the town and head right. The Old man will be there in front of a building/Inn. If you hit the Saber Jump location, you've gone too far.

For anyone else still trying to get 100% also found some suggestions for hard to find log entries from this guide from psnprofiles com. Link below.
https://psnprofiles.com/guide/17783-fatesamurai-remnant-trophy-guide#48-the-all-knowing

Do I have to do the flames of resentment ending a second time after getting entreat the darkness for the all knowing achievement?

Agreement with takao: I start from Prologue, and then after meeting with Takao for the first time and go back to home, and then able to open map again, choose Yoshiwara. Saber will ask question something about Agreement with Takao https://i.imgur.com/4gNN1Uc.png and question "Do you really wish to head to Yoshiwara?" I chose No but idk if it matters (also I remember when I finally got this, somehow the HUD didn't tell that there's logbook update but I checked and it's there)

want to add my experience on getting some those missable entry (all of those I got in NG+, idk if works on NG)

Terminology-Locations-Gongenyama Castle: when you first time unlock Kanagawa Port and then go back home, go to Kanagawa Port again and talk to people (I think it's the first person I can talk; from the entrance go straight a bit then go left). It should trigger the Gongenyama Castle logbook entry

Biographies-Other-Mori Souiken-Page from a Journal: I got this by: At the end of Chapter IV , I chose Pursue Assassin, then do the Spirit Font Conflicts and go to Kanda . GO TO THE ITEM LOCATION FIRST https://i.imgur.com/JsvjXSx.png before go to the quest location. Then you progress and fight rogue assassin then ushi gozen and then you will get the logbook entry

Where is Gongemyama castle?
Thats the only one im missing hopefully...

Can anyone help me get the entry Agreement with takao is seem the author can't even explain this properly.

"Agreement with takao" is poorly explain. Needs more details since this is missable and obtain it is quite difficult and annoying to get.

guys i have all the entries and the 100% in story and disgressions but dont have the trophy what happen?