We should probably get the language correct here then to clarify. It seems you are concerned about Cities and not settlements directly. An Opt-Out cannot affect any settlement unless it surround its. If it surrounds it then that is a CoC issue and it can be removed. Otherwise no settlement is at all effect in any way at all by an opt-out.
Cities might be effected but honestly that is a non-issue now because of the buffer system. If people leave or plots open up, the buffer system can break up a City into individual settlements. So yes that is a concern… but for many people think we need to redesign Cities anyway using some other system.
Why? Because the current design isn’t really creating a true city - it is just taking settlements near each other and making a city. And to be honest, some of those people don’t even want to be part of the city.
The primary reason a person wants to keep a city is either because they are the Mayor and their ego is important, or they are trying to abuse and take advantage of the prestige system to get the most footfall or become Viceroy of the planet. Cities don’t really provide any benefit to the game so we shouldn’t be stopping things that help remove conflict from the game.
If people want cities they need to follow this model and support it - Thought Experiment: Remove Greater Settlements and only keep Guild Settlements