No, I don't agree entirely. The more I play (my 6th, 7thish playthrough now), the more I understand.
The boys were killed by mandus, not long before, to save them from the upcoming century.
To whom are you refering by three people telling the story? Obviously Mandus, but who else? The machine/engineer? The professor? The children?
Notes from others (the children, the truck driver, etc.) are valuable to either the story or solving the puzzles, but I don't think they're contradictory.
I don't know about the unused files, I might look into that, sounds interesting