How about this, lets take the elder scrolls series and changed it, the lore and cannon of it, and see how many people get angry?
In the Pocket Guide to the Empire (pre-Oblivion lore), Cyrodiil is described as "endless jungle". In Oblivion, Cyrodiil appears as temperate forest. Bethesda do just change things whenever they feel like it. And yes, a handful of people got very angry indeed, and everyone else just got on with playing the game.
thats assuming that the only reason that it would be in canon is because there was "an" alien refed in a n easter egg...
According to the http://fallout.wikia.com/wiki/Alien_Crash_Site:
"The Alien Crash Site appears in Fallout 3. However, crashed alien spacecraft are not new to the Fallout series. A crashed flying saucer appears in Fallout 1 as a special encounter. In the original encounter, it is clear that the spacecraft had been at least known to Earth, as it bore a "Property of Area 51" sticker. Like the Fallout 3 encounter, it was also the source for the unique Alien Blaster.
In Fallout 2, the Alien Blaster can be bought off a random encounter merchant provided the player has a high enough luck stat. No flying saucers or alien crash sites are part of the Fallout 2 game world, however a crashed spacecraft of a sort does exist as the Federation Crash Site special encounter.
On close examination of the ship's cockpit, there appears to be three seats, there could have been more aliens that survived."
My point was that when something is repeatedly referenced, it can no longer be considered as a one-off joke, but a proper part of the game. It's like the difference between a cameo and a recurring character.