Again, I'm not sure what to say, it's just what I experienced. The save is 100% mine (currently at 793+ hours of my life) and as far as "cheating" goes, I've only used some common/more "tame" mods (like the All-talk or the expanded library ones, didn't touch the ones like the mimic room or I think there's one for infinite items?)... and I guess the built-in Ruler Ruler for grinding purposes, but that too was only after I beat the game. I don't even know how to use cheat engine.
I understand that I shouldn't have gotten the achievement (when I saw the warning message in Part 2 about it, I even made a separate save file for me to go back and get it legitimately), but I just did. If that was indeed a bug, then I apologize for the misleading info, I really thought it was an oversight in the code or something like that.