I had to go to Vegas yesterday for the day so I had eight hours of driving time to fill (4 over and 4 back) so I listened to several older DiFs again and one of them was Super8. After listening to your guys commentary again I think I realized the disconnect.
If you're expecting an alien movie then the kids story doesn't really fit in. Likewise if you are expecting a story about the kids trying to finish their film then the alien story doesn't seem to tie into that. I think you are victims of the advertising. You are trying to find the connection between the footage the kids shot and how it affects the alien plot, or visa versa. But you need to look at it through a different lens. It's not about the alien and it's not about the film. It's a boy meets girl story. In order for the two of them to get together, everyone has to learn how to let go of all the issues they have. The film they are making and the alien train crash are simply the devises used to get the boy and the girl together.
In the beginning of the movie it's the need of a female lead that first brings the girl into this boy's world. Then later it is the alien plot, specifically her being abducted, that finally brings them together in a meaningful way. It's the girl that teaches him to to stand up and not be pushed around by his bossy friend. Its his like for the girl that finally drives him to confront his dad. The plot revolves around the boy getting the girl.
I think the advertising set up an expectation that the footage they shot would have something to do with the alien plot. But if you look passed that with a clean slate, then I think you can see what the movie was really about. The boy gets the girl. And in order for that to happen, everyone had to learn to let go of their issues.