I personally take the view that pretty much everything matters. It's just more fun that way... :D
As far as the MSP goes, I take everything as possible theories but don't really hold it as fact. If I'm cruising through the terminals and notice something strange I have *no* problem rejecting all known theories for one that makes more sense.
Much of the stuff in the story pages are obviously out-dated or end right before the puzzle was solved. The last time I checked, the "You" page still doesn't come right out and say that you were a cyborg. It's still a bunch of outdated theories.
As far as I can tell there is no mention of a particular email I ran into, makes no discussion of it, nada. Is it real? I haven't a clue...
That being said, I don't think we'll ever know it all. We'll always just have a bunch of theories...
Not unless they release a "Secrets of Marathon". That would be interesting.