The reason Eliezer's views are commonly mistaken for relativism in the manner you describe is because most people do not have a good grasp on the difference between sense and reference(a difference that, to be fair, doesn't seem to be well explained anywhere). To elaborate:
"Define good and bad and so forth in terms of what human beings, in fact, value" sounds like saying that goodness depends on human values. This is the definition you get if you say "let 'good' mean 'human values'". But the actual idea is meant to be more analogous to this: assuming for the sake of argument that humans value cake, define "good" to mean cake. Obviously, under that definition, "cake is always good regardless of what humans value" is true. In that case "good" is a rigid designator for cake.
The difference is that "good" and "human values" are not synonymous. But they refer to the same thing, when you fully dereference them, namely {happiness, fun and so forth}. This is the difference between sense and reference, and it's why it is necessary to understand rigid designators.
This is the definition you get if you say "let 'good' mean 'human values'". But the actual idea is meant to be more analogous to this: assuming for the sake of argument that humans value cake, define "good" to mean cake. Obviously, under that definition, "cake is always good regardless of what humans value" is true. In that case "good" is a rigid designator for cake.
Why is cake a referent of good?
...The difference is that "good" and "human values" are not synonymous. But they refer to the same
There seems to be a widespread impression that the metaethics sequence was not very successful as an explanation of Eliezer Yudkowsky's views. It even says so on the wiki. And frankly, I'm puzzled by this... hence the "apparently" in this post's title. When I read the metaethics sequence, it seemed to make perfect sense to me. I can think of a couple things that may have made me different from the average OB/LW reader in this regard: