Its Canon if bethesda says its canon... not realy anything we can do about it..
and yes Aliens arent "new" to the searies...
Well, that's thing. They haven't technically "said" anything about events are canon from Fallout 3. Realistically, we won't get any of that information until we're playing Fallout 4.
For example - is it "official" canon that Megaton was, or was not nuked in Fallout 3? (Well, that's an easy one - I'd put money on, if it even comes up in Fallout 4, Megaton still being around. Because nine times out ten, the sequel will tend to go with the "good" ending.) I can't really go into much else without giving away spoilers, but take literally any sidequest in Fallout 3. What's the "canon" resolution to that sidequest?
The answer is that most of them aren't going to have an "official" status. Chances are that Fallout 4 isn't going to be really concerned with what happened to the player in the previous games - with the exception of possibly a few major elements (ie, what decisions you make at the end of the game, etc...) And any of that's assuming that anything at all gets any definitive reference in the next game. Take Fallout 2, for example. It's canon that in Fallout 1 the PC helped Shady Sands (or that they at least survived,) so that they could form the NCR. But there is no canon status for what deals the PC may have made with the Water Vendors in Fallout 1.
For Fallout 2, I don't even see there as being any canon status for any of the events in that game, at all. Because there's nothing in that game (that I came across, at least) that
has to have happened for the events in Fallout 3 to take place. There is no official story there, as far as I'm concerned.
So the canon status of anything from Fallout 3 (MZ, any of the DLC, or even any of the quests from the base game,) is up in the air until and unless it gets referenced in the next game.
So again - if there's no mention of the events of Mothership Zeta in Fallout 4 (or any other subsequent games,) then it simply isn't canon. (And in this instance, I mean canon as in "the things that officially happened in the previous game." Just because it's not canon doesn't mean it can't have happened, or that it doesn't officially exist. It's like Schroedinger's cat... Or a politician saying "no comment.")