I see. Kind of questionable game design for the developers to put non canon elements into the game in such a way that they are encountered during normal gameplay. But here's the really important thing. We have a precedent of the UFO in Fallout 1 being a special encounter, and special encounters are said to be non canon. The UFO in Fallout 3 is also a special encounter; the exploding ship is a random event and the crashed ship is a clear throwback to FO1. Therefore, since Mothership Zeta is one large special encounter, the entire DLC is non canon.