Well, here is my answer, take it for what it's worth.
It's as much about aliens as LSD.
Some people aren't oblivious to the Bill Hicks referrences.
Tool has done it's best to let people in on the jokes, some just look beyond it.

You'll also note that while Bill Hicks lampooned hippies and druggies, he also was the first to say he did his share and enjoyed them, and while he lampooned bubbas who carried shotguns to UFO sightings for fear of abduction, he would be the first to say he saw a UFO and might have indeed been abducted himself.

That's the thing, if you catch yourself saying this song is defintely about A as opposed to B, you might very well be missing the point altogether. Who says it can't be about both?

In fact the only hard evidence we have about this song are the lyrics, music, some referrences from Blair and the Alex Grey comments.

What does it tell us? Well clearly Dave shit his bed while camped out at Area 51 tripping his balls off. That's the underlying theme. Then Maynard like any writer trying to convey a message or theme will trick up the lyrics as to not be completely banal. He wrote the narrative to where if you were a head trying to dig deep, you'd be spinning wheels trying to understand all the musical self-sampling and "message" when the narrarator clearly states he can't remember what they said, he forgot his pen, he metaphorically and literally "shit the bed". In other words, there is no Rosetta Stone here, it was lost. It's just a funny story amped up tenfold, to add the "needed" flavors. Much in the same way The Balls of Satan needed to be in German.

The aspect of ET's is part of the narrative, it conveys the exact same theme as the LSD trip, because either this is an actual verbatim true story (we all know it's not) or it's an expansion upon a funny story (Dave shit the bed) with a message about hippies disappearing up their own arse trying to decipher hi-hats and sequences and why the synth from Reflection pops out of nowhere "woah dude!!", to add the proper mysticsm to this satire, we have the UFO angle. It is as much the fabric of the song as any of the rest.

I think it's a satire about those looking for esoteric hidden messages, when clearly the intention of the song has at least a very large dose of humor (Bill Hicks). The message is stop spinning wheels, metaphorically shitting the bed, because one day you may have the chance to change yourself, if not others and you shouldn't waste time trying to look for anwsers elsewhere, you were lead to water, did you not drink "Think for yourself, brothers and sisters".

The idea here, the humor, the satire is that Tool knows that people will see into their own ideas of the Tool "mysticsm". It's an exposition, you aren't really thinking for yourself if you think this song is "about drugs man...", the irony is in the song itself, plain as can be.

Back to the Bill HIcks thing for one second, where do his rants fit in with what I am saying? It's the same effect. The yahoos grab their guns to shoot the little green men from the sky before they get anally probed, the 'heads' are too busy trying to sift thru obvious comical narratives looking for passages about mankind (or some shit). The Bill Hicks underline here is that 1-nobody is saying aliens aren't real, that this shit doesn't happen, the joke is that it's always some gomer that it happens to. 2-The fact that said narrarator couldn't "hold his", had he not been trippin balls he'd have the message to mankind. That's not anti-drug, it's anti-fool.

There isn't an admonishment of either here (drugs UFO's)because the implication is that Tool knows that the fans paying attention know that they dabble with hallucinogens or at least used to, and at the least have an interest in ufology. So the satire works, because they've got at least half of the people hook, line and sinker, trying to decipher the Rosetta Stone in this song, even when it's clearly stated it's lost (never was). Shit the bed again=missed the point again.
The real point here? Enjoy the song, have a laugh, stop looking past the obvious.

Faiip has nothing to do with drugs either, does it? What about aliens? Well the joke is implicit here as well, the Art Bell call was a hoax, trippy weird music to send one part of the crowd one way trying to unlock hidden meanings or just sacred shitless, the Enochian title, same effect. All the while the call on the song is a hoax. This is a joke. How could Tool end this "opus" Lateralus on a joke? They are trying to let you in on what they are doing. Not taking themselves that seriously.

The cow with the head up his ass on the Undertow package=joke, Rosetta Stoned=joke, it's as much about LSD as it is about aliens, because in truth it's just a satire. The whole idea of Tool is in this song, the guys who said they were about the fictitious lachrymology, sent drones off buying into it, all they had to do was play the part. They call themselves 'Tool' for a reason, and lachrymology isn't it. The joke is still alive and well, the next time someone is at a Tool concert, tripping out at the deep message of a transcendant joke, I'm sure Maynard will have a laugh as he sings "shit the bed" and knows some bloke out there is saying "right on man".

It's not all a con, but that's the whole idea, get past the artifice, the darkness, the imageries, you'll find a rock band trying to make meaningful music and trying to let you know that's all they are doing. They aren't trying to give you the answers, they are trying methods to get you to find them out for yourself.