99.9% of Marvel comics takes place in NYC. Every time Green Goblin goes on a murder spree the world waits for Spidy to take him out. Where in reality ever hero from the Avengers to the X-men to the Punisher would be all over his shit in 5 seconds.
In DC at least all he heroes have different cities so it's makes more sense.
That's comics. As you say they are separate until they aren't.
Yup. In movies, cartoons and comics. It's really just a matter of convenience and you have to accept it.