This is an excellent, excellent point.
I was told, a while back, that there are actually three stories: the story in your head, the story on the paper, and the story in the reader's head.
For the writer, her job is to try to get the story on the paper as close to the story in her head as possible. She still can't control the story in the reader's head, because it starts at the words on the manuscript and grows from there based on the reader's history and experience. But if the story on the paper doesn't match with the one in her head, the reader will end up nowhere near the story in her head. Note that this situation shows a problem with the words on the paper, and is not necessarily a failure of the story itself.
The ability to somehow separate the story on the paper from the one in your head is a crucial ability, and one I still have not been able to develop to any degree. I still try with every story to read the story on the paper for what it is, on the paper. Maybe one day I'll actually figure it out.
Overall, a great post. Go read it!