For me, how I see it is that the boy and the girl in the story somehow has an "unspoken" and "unknown" feelings with each other and they might not have an idea about it or vice versa.
The story is quite hard to understand because it really doesn't say a lot. The class had many theories but nothing's seems to hit the bingo regarding what's their relationship and what's the point of the story.
For me, I'm quite convinced that they both have feelings for each other because 1) The story that she wrote on the boys computer, 2) the boy assumed that it was for him, and number 3) when their family and friends thought that they were a couple, they didn't disagree or correct them. They didn't do anything and let them be.
We're not really sure whether they are a couple or not one thing's for sure, they are close friends and very much comfortable with each other. Close enough to let the girl inside his room and use his computer even if he's not around.