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.
The entire DLC being non-canon would make me SO much happier but it's not considered as a special encounter. Bethesda made aliens canon, making them take away existing people and just ruin the lore with Log #17 which could also be called The Log of Logic Destruction. And also it's not questionable game design. There are non-canon events happening in games every single goddamn time. It's a game with CHOICES. For all you know, everything could be non-canon because the Courier killed this guy or LW stopped caring for the survival book. Those choices still happen in normal gameplay because it's player choice, and special events happen because they just do. They could just be alternate reality type of things that in this alternate reality distract the protagonist while in the canon world they do not. It's pure logic.
Any choice you do in... let's say... Fallout 1 for example won't matter unless they're truly canon considering what Fallout 2 tells you since it's already happening after it. For all you'd know, the Vault Dweller NEVER saw the UFO in his entire life and maybe he was hallucinating at one point.
As I said. It's not questionable game design. It's game design that makes the game more enjoyable and while breaking from the world's immersion to some pop culture reference isn't exactly great, atleast they're subtle enough to be fun little things to remind you that you're playing a game, something to entertain you while providing you a world to make choices in, think about for a long period of time (literally the whole point of this forum, talking and thinking about Fallout since the
90s!) and expand your knowledge. Mothership Zeta is NOT subtle, it RUINS the lore that people love and most of all... it's a frustrating, buggy and corriodor-shooter-in-a-RPG-y DLC that shouldn't of been released! This is NOT a subtle special event, it's a canon DLC that shoves itself IN YOUR FACE and tells you, with no regrets, that it's canon.