Another problem is people don't want to have to lock every single thing they have up in an underground vault. Raiders have a tendency to clean people out for no other reason than to troll them. My excess stores of food aren't particularly important but I don't feel it should be necessary that every stack be under lock and key.
Additionally, what is the point in towns of people can come and go as they please? Even if I have everything locked down, I don't want some random person running around inside my walls because they found a way in.
All this requires fugly domes or an insane amount of effort to create an enclosed city that still looks good. It's unrealistic. I'm a fan of Raiders being able to do their thing but in a place full of advanced raiders it renders normal gameplay unenjoyable if every move is in paranoia. Yes, that thrill is part of the fun but also part of the reason fewer stay after falling victim to raids.