For example, let's take quest markers in Dishonored series. Quest markers can be disabled, but this feature is turned on by default so most players aren't going to disable it. After all, videogames are about optimization, finding a path of least resistance and "gaming" the system. If the game gives you options that are so OP you may as well call them cheats, players will use those options even if it may rob them of fun in the process.
Another issue is that when starting the new game players aren't going to be familiar with game's systems. How can they make decisions on which options to toggle on and which to toggle off when they don't even know how the game works? How do I know what tier of "AI perception" the levels were designed around?
And, obviously, there's also a question of "intended experience". How can you discuss the game with other players, when there's always a possibility that you played it on a big man mode, while they picked an easy option and also skipped most of the difficult content? One can say "i reduced enemy's stats because in my opinion they were inflated, and this reduction made the game less of a slog", but what if the tanky enemies were a part of intended experience? What if the game tried to teach you how to properly cut through armor, or use special abilities to reduce resistances, or to properly build your damage dealers? Can you really say "I finished the game!" when you basically skipped a possibly important chunk of gameplay?