You know the old saying, "Fate can be a cruel mistress." Bill Warren's letter is not in the excellent Agel book on 2001, although Kubrick wanted to include it. It seems he misplaced the letter, had his assistant contact Bill to see if he had kept a copy but, back then, letters tended to be a one-shot thing and there was no carbon copy or Xerox on hand. So those initial insights are lost to us. However, we do have a Bill Warren commentary on the link in my initial post:

"I finally got around to watching that odd site that attempts to explain 2001. I think every idea in it can be justified by the movie itself--even if I don't agree with every idea in it, such as using the word "supernatural" or citing the "fourth dimension" as the room where Bowman is confined at the end of the movie. Also, this explanation doesn't take into account such things as names (Bowman, Poole).

"I think it's dead wrong in saying that it is "not the monolith itself" that affects the apes who touch it; I think there's no question that it is the monolith--otherwise, why is it even in the movie? It jolts the apes just a bit on their evolutionary path "upward." The explanation doesn't take into account the third and fourth monoliths, but that lack doesn't affect the overall set of suppositions.

"Yes, we encounter the second Monolith (on the Moon) when we're at some kind of evolutionary dead end. And I do like the idea that we've allowed ourselves to become too dependent on machines--but I don't buy the idea that HAL represents a rebellion by machines against Man.

"There are some very odd ideas tossed in, like the Moon ship (the round one) being described as "sinister." I don't see it. And yet this piece misses the phallic symbolism of the shuttle docking at the space station.

"Also, though they don't show very MUCH, the men on the Moon do show some fear and some wonder when confronting the Monolith.

"I don't buy at all the idea that going into space has reduced men to an infantile level, so we require toilet training and have to eat baby food. ON the Moon, people eat solid food ("tastes like that, anyway"). We were originally to have shown actual children on the Moon; stills exist. This idea doesn't even fit into the rest of the ideas in this piece.
This piece skips over the alien motivation, focusing entirely on human evolution, which is reasonable and can be justified in the movie itself. On the other hand, claiming that those aboard Discovery are merely "maintenance men" is an error--we don't know what everyone's purpose was once Jupiter space was reached, since by that time HAL has been shut down and Bowman's the sole human survivor. But there had to be a reason for the ship to have a crew of six beyond all of the people merely being janitors. This theory HAS to skip over that, though, since they're trying to emphasize the wobbly idea that men have become ENTIRELY dependent on and even subservient to machines. I have no doubt that elements of that played a part in Kubrick's thinking, but this piece also tends to reduce the complexity underlying some of the film.
HAL does not think he's alive, but he's AWARE, and doesn't want his awareness to end. However, Kubrick wants the AUDIENCE to regard HAL as being sort of alive.

"The writer (or writers) skipped over the whole Trip sequence; not sure why, maybe they didn't want to confront the possibility of actual aliens doing actual stuff. KUBRICK wanted to dodge that, too, but couldn't entirely do that and still make sense.

"This was very interesting, especially considering its brevity. But why don't Bowman and Poole look like Dullea and Lockwood?"