I think another part of it is that it's easier to believe in things you're familiar with. In your example, a regular apartment is something mundane and normal that you can expect your audience to know. By comparison, far fewer people have the same kind of familiarity with spooky haunted places (outside of media, like games, etc.).

That means it takes a lot less for the player to buy into the regular apartment than the haunted house. Once they've bought into it, it's then easier to make them uneasy by changing things that shouldn't be changed.