Bethesda needs to admit that Mothership Zeta is not canon.
I think they will. Even if its unintentionally.
This is the way I look at it. If MZ turns out to be canon, then its assumed that the LW would have given all of the Alien technology to the CWBOS, since he
apparently worked so closely with them. <_<
So therefore, if MZ is canon, we now have the CWBOS armed with Enclave technology acquired during the war (including vertibirds, APA, plasma) as well as alien weapons from MZ (disentergrators, atomizers etc)
and full access to Mothership Zeta and all technology aboard it, including, but certainly not limited to: http://www.youtube.com/watch?v=bDs64HuHL7M. Guess what that would mean? Nothing can stop the CWBOS from taking over the world.
My guess is (my hope is) that Bethesda wouldn't be that stupid to create a god-faction like that. Since I believe they will want to revist the CWBOS again. Its also safe to say, if we see the CWBOS in a future game and they
don't have alien weapons/tech that MZ never happened in the game universe.