I recently went through the base game with the mod installed, as I like the change in the world machine's text colour to purple, and the actual threat of Niko dying if I close the game early. Naturally, I didn't expect anything about the base story to change.
That was, until
The world machine grills you at the top of the tower for changing the games files in those windows pop-up messages, before asking you how many times you've played through this game, like the thousand games before it. It tells you that someone that does that doesn't really care about Niko.
Making the player guilty for having disrupted Niko's happy ending by downloading this mod was one of the techniques I was looking forward to seeing in the new story content of the mod, which I did get some of. The instance above was perfect though because it hit me in a moment I was complacent with a "hey you, I know what you did".