You suggested we take the song at face value, and then go on to assume background information about the band who wrote the song. That's quite the opposite of taking the song at face value. I'm not even nit-picking on some little aspect of the definition. You're doing the exact opposite of what you suggest we do.

Fact of the matter is this:
If we take the song at face value, the song does mention the X-Files, ET, Area 51, etc., which all hint to aliens.
If we don't take the song at face value, and look at background information about the band, I look back to Lateralus and remember the track Faaip de Oied, which also hints towards aliens, and makes it very hard to instantly rule aliens out for this track, Rosetta Stoned.

I am not trying to say that this song is most definitely about aliens, but I AM trying to say that it is ABSURD for you to try saying that the song is most definitely not about aliens, just because you have a feeling that Tool wouldn't write a song about little green dudes flying around in saucers.