All depends on the author. Partly whether they use a real world setting or create their own--like Jim using Chicago, compared to Charlaine Harris's Bon Temps. Least I'm pretty certain that one's made up. Also, just depends on the author. I believe that Harry's apartment building is completely made up. But in comparison to that, Patricia Briggs has told a story a couple times about needing a house to use for one of her books and a friend said she could use their house. Patricia's said before that all the houses in her books are actual houses in the Tricities area. She just doesn't give any specifics as to where they actually are.
Generally, if it's a residential place, I'd say to fudge that in a way, but if it's a landmark and/or recognizable, don't change it. If it's both...not entirely sure on that one.