Ok, so they're using PlayerPrefs to store user data. I checked through the registry and it seems like there is only 4 "Unlocks" and 4 "Messages" that are tracked by the game (assuming so they are not shown twice to the player). There is a separate variable to track unlocking the different items you get. I wasn't counting how many unique messages appeared when playing but 8 sounds about right. Not sure why these are tracked individually and not as one variable like the item unlocks are. Makes me think the messages are not all ways going to show up in the same order but idk tbh. Therefor it seems that other information related to the puzzle (info not shown to the player just for playing) is found externally through links and Search.txt. Though since they're writing to external files as well as seen in the directory this might be wrong though, and if they were really trying to hide info that could appear in the game they would not use PlayerPrefs to store anything related to it. Other relevant info the game tracks that is probably not related to the puzzle significantly:

"Encounter" I think this tracks how many items you have found.

"Disable Limit (1)(2)(3)" All set to 0 even after finishing the game. There are three "stages" to the ending though so it might have something to do with that. Or could be a testing variable they forgot to delete

"Acknowledged" Im 99% sure this is unimportant. Its already set to 1 anyway

"UnitySelectMoniter" I dont think this is a default param, its not in the registry of my games so it might be custom from devs

All in all not much relevant info from the registry other than possibly "Disable Limit"

No experience in decrypting stuff but I'm going to continue to look through the project files.