Whose to say if it was a real alien blaster or one made to look like one. It used standard energy microfusion ammo. These encounters took place days (or weeks) into the deserts, and the PC's accounts may be suspect... Out there with no water (sometimes). The contention isn't that there are or aren't aliens in the Fallout setting, it is that they were never allowed to be proven to be. It was always an uncertainty ~until FO3...
My own preference is that they are real, and exist in the Fallout setting, but that they never interact with mankind, and for the most part, never even come to Earth. If the PC sees one, they should have reason to doubt what they saw. (And of course, that the aliens never have any involvement with the war.)
I think that the alien crash site in FO3 is a classic example of copying a thing without understanding it. Fallout had it, so FO3 had it too; except that the location and circumstances matter, and they don't seem to have been considered in FO3, or NV.
This is the kind of thing that gets the Fallout series fans the reputation for being unpleasable, and the reasons for contention are always dismissed or ignored in favor of just calling them irate.