There is a lot more to it than that, and you know it.
The alien stuff is the only "easter egg" with long-lasting and permanent impact on the first two games, through the alien blaster. Blasters are sold in a store in FO2, and used through the game in all cannon events, if you desire it. I know I read on NMA that a character and computer both mention aliens as well.
Whether Black Isle meant for them to be cannon or not, they were in the first two games enough where seeing them expanded on in FO3 is not really surprising or disturbing.
P.S. Of course DLC is cannon... geez.
Alien Blaster is definitely an easter egg in the first two games.
What store can you buy it from? The only ways I know that you can get the blaster in FO2 are: You can get it in a easter-egg/special encounter crashed ship, have specific stats in a specific order while also getting lucky from passing a check after hacking a specific terminal in the oil rig, or from a merchant who you may encounter on one square of the map if you continuously travel around that square...who will randomly have the weapon, and you only find out AFTER you bought whatever he is selling. It isn't common, and most people will never even know it exists at all unless they just happen to stumble upon it by sheer chance/luck.
A character in Redding calls Wannamingos "aliens", because from his point of view they are strange things, but they are really just mutations. They are terrestrial. Are you talking about the Hubologists?
The computer mentioning aliens, I believe is in reference to 'alien technology', meaning foreign/unknown-at-the-time technology. I never took that as it being built by extra-terrestrial hardware.
While it isn't surprising that Beth is expanding on aliens in FO3, it certainly leaves me scratching my head as to why.