Across contexts, I generally abhor things that can be said to limit "user freedom", but there's a thing about psychology that frequently justifies exceptions in games: __choosing something can have emotional strings attached apart from the thing chosen.__
For one example, I once had an argument with the developer of Prismata about his decision to hide rating from players below Tier X. I argued that this was insulting to enthusiastic new players, that his fears about new players getting discouraged by seeing it were unfounded, that this just forced them to guess anyway, and that if his fears couldn't be allayed he should just make it so players had to click a button to see it. While most of my points were valid and I totally still stand by my position, the last one was fallacious.
Having the button available and choosing not to click would feel very different from just not having the information. Not only might this cause upset to some people who'd have to deal with the knowlegde that they were too afraid to click the button, and might think themselves pathetic (I would); but having the ability to find out so readily accessible would make the uncertainty so nagging that probably no one could resist clicking it. If I had had a better understanding of psychology at the time I would have realized this.
Another and more important example I discuss in The Importance of Turn Timers.
A third example would be enforcing diversity of playstyle. If you're making a game where the player can choose a character to play as or a faction in a real-time strategy game, if you don't do anything I expect you'll notice playtesters forming a favorite and always picking that one, to the end of not seeing a lot of what the game has to offer and skewing their balance opinions due to this stilted experience.
No one wants to choose to not play as their favorite. But if you were to take that control away and make the players always random races in your RTS game, you wouldn't have those problems. I expect that more than griping about being made to play as one they don't like they'd learn to like them all in their own way (Prismata's unit selection system has absolutely had this effect on me) - because a lot of having a favorite in a game where you choose comes from being more experienced with it. If you happen to have some good experiences with one in your early days you're likely to keep playing as it and it spirals into a total favoritism since nothing ever forces you to play with the others.
As a fourth example, this is a potential justification for not allowing the player to edit enemies' stats at will. While players would rarely use it because they aren't self-misunderstanding morons, having the ability be so granular and so easily accessible might harm the enjoyment of playing the game the intended way:
What if the game's designers made a mistake and a section is just poorly balanced? Almost every game has some of those, but at what point should the player draw the line and change it? I don't even necessarily mean making it easier. Maybe you want to change something to try to make some of the decisions less trivial? If you do it you won't be able to escape the nagging worry that you made the game worse and you're going to regret it later, and if you don't you won't be able to escape the nagging worry that you're missing out on a rare opportunity to exercise a power than few games give you and you're going to regret trusting those idiot designers. Even worse: it's likely that neither worry will ever be put to rest because you'll never find out for sure which choice actually makes the game better balanced.
Also, with the settings so granular, the inhibition to use them is much weaker. In a game with rigid difficulty settings you're losing a very significant pride token if you lower it, but in a game where you can freely adjust anything you'll live with the knowledge that it's impossible that the way you're playing the game is the perfect balance for you, and so you might be very tempted to tamper with it in an effort to make the difficulty a better fit for you.
Not to mention the issues of, "I want to play the same game everyone else did so we can discuss our shared experience, but given it's so easy to modify and there are infinite unnamed possible versions, how do I know they didn't modify it slightly?"
With a few rigid difficulty settings the settings are named, which means players can still talk about their shared experience meaningfully. But if you can arbitrarily adjust any game balance variable then difficulty names are impossible, and so it's impossible to know how your experience differed from someone else's without recounting everything you did.
I'd of course never raise this as a defense of practices like single-difficulty games and no pausing, because those are concerns of accessibility and not of how the game should work while you're playing it.