In a way Cow Tools was too simple rather than too hard, so people thought there must be more to it.
I don't think the joke itself is a bad idea. I remember The Simpsons doing the room full of monkeys on typewriters where one comes up with "it was the best of times, it was the blurst of times" which in a way is a similar joke, right? i.e. Not a good result, but funny because it's still much more than you'd ever expect in reality.
The joke was a reference to that pop culture idea which pointed out that if the infinite monkeys thing is real, there should also necessarily be products that are very close to great works but not quite right.
Yes, but the additional joke is that a room full of keyboard-mashing monkeys haven't only produced random nonsense, but have almost produced something well-crafted - much like with Cow Tools.
There's an additional layer to the Simpsons joke, with Burns dismissing what's really an incredible result (almost the opening line from A Tale of Two Cities) as useless just because of one small error. The Cow Tools equivalent might a farmer holding the saw, saying "This isn't even sharp."
Given that the monkey is sitting there smoking a cigarette, clearly stressed out, chained to the typewriter, I wonder if there's also a third or fourth layer to the Simpsons joke where the monkey represents the scriptwriter and Burns represents Fox. The equivalent for Cow Tools would be, er, Cow Comics, and it's just XKCD art quality comics on the Cow's table, and the farmer complains that the drawings aren't very good.
Specifically, the Far Side panel plays on the idea of the fact that cows would have a cow-centric view of the world and would likely develop tools that were alien to us. The other part of the 'joke' is that cows don't build tools (afaik). edit: I think the "3rd" part of the joke is that the tools look like shit, which is what you'd expect from even the most talented cows.
The humor of the space alien joke is similar in that it's pointing out the difficulty that everyone has in understanding how others (other people, other species, etc.) view and describe the world.
[0] https://en.wikipedia.org/wiki/Cow_tools