It may be a reference to Godzilla, but the track could have been created by an irradiated creature. There's nothing explicitly stating that Godzilla made it in the context of the game world.
http://fallout.wikia.com/wiki/Fallout_special_encounters
http://planetfallout.gamespy.com/wiki/Fallout_1_Special_Encounters
http://resolution-magazine.co.uk/issue2/article_falloutretrospective.htm
(Now, I can keep beating this to death if you really want, but it was obviously there as a reference in the same way all their pop-culture special encounters and other references happened. They never said "Oh hey I'm the guy from The Holy Grail" you simply either got the reference or you didn't, and you moved on.)
I'm pretty sure the alien crash site is a real part of the game. Some might argue that it's not canon, but it's there so it's canon... whether we like it or not.
It's a special encounter, plain and simple. Like it or not? I like it. But that doesn't change the fact that it's a special encounter.
As for the Fallout 2 encounters, I have a hard time not finding them... especially the bridge, the Cafe of Broken Dreams, and the angry posters attacking a spammer demanding multiplayer. These are the ones I hate the most, I might add.
Those three, Cafe of Broken Dreams, Unwashed Villagers and the Bridgekeeper were the only three super-common encounters and I'll agree that I wish they weren't. Something tells me (and this is just a guess) that they were broken. Meaning, I think most special encounters were only meant to happen once and then be toggled "off". The thing about the Unwashed Villagers though, is that this was the Interplay/B.I. team showing their appreciation for their forum/internet fans and including a pretty random moment from the old boards in their game. I thought it was quite brilliant, actually.