Actually I've learned something: I'm pretty sure it's impossible to get everything in the encyclopedia, even with in-game cheats. I used a cheat tool called Mtool that the dev recommended a while back, looking at certain things in the game using that program, the way that things like items are listed in the code almost perfectly line up with how they're listed in the encyclopedia.
Some of the entries are dev tools that only they would see or use, that aren't meant to be obtainable in game, some are old features of the game that were removed from actual gameplay in updates, but left in the code partially, and they line up exactly with where the gaps are in my Encyclopedia on my 100%, all secret bosses, all quests save.
I say don't sweat the Encyclopedia percentage, and just focus on the quests and challenges that are actually implemented.
The missing bits would be things like equipment that's only used by NPCs or temporary party members, or skills that are used by enemies, or used for debugging and dev purposes.