The paper's goal is not to discuss "basic UFAI doomsday scenarios" in the general sense, but to discuss the particular case where the AI goes all pear-shaped EVEN IF it is programmed to be friendly to humans.

That last part (even if it is programmed to be friendly to humans) is the critical qualifier that narrows down the discussion to those particular doomsday scenarios in which the AI does claim to be trying to be friendly to humans - it claims to be maximizing human happiness - but in spite of that it does something insanely wicked.

So, Eli says:

The basic UFAI doomsday scenario is: the AI has vast powers of learning and inference with respect to its world-model, but has its utility function (value system) hardcoded. Since the hardcoded utility function does not specify a naturalization of morality, or CEV, or whatever, the UFAI proceeds to tile the universe in whatever it happens to like (which are things we people don't like), precisely because it has no motivation to "fix" its hardcoded utility function

... and this clearly says that the type of AI he has in mind is one that is not even trying to be friendly. Rather, he talks about how its

hardcoded utility function does not specify a naturalization of morality, or CEV, or whatever

And then he adds that

the UFAI proceeds to tile the universe in whatever it happens to like

... which has nothing to do with the cases that the entire paper is about, namely the cases where the AI is trying really hard to be friendly, but doing it in a way that we did not intend.

If you read the paper all of this is obvious pretty quickly, but perhaps if you only skim-read a few paragraphs you might get the wrong impression. I suspect that is what happened.