I was about to cite the same sorts of things to explain why they DO disagree about what is good and bad. In other words, I agree with you about utilitarianism being wrong about the structure of ethics in precisely the way you described, but I think that also entails utilitarianism coming to different concrete ethical conclusions. If a murderer really likes murdering - it's truly a terminal value - the utilitarian HAS to take that into account. On Eliezer's theory, this need not be so. So you can construct a hypothetical where the utilitarian has to allow someone to be murdered simply to satisfy a (or many) murderer's preference where on Eliezer's theory, nothing of this nature has to be done.
That is a problem for average-over-agents utilitarianism, but not a fatal one; the per-agent utility function you use need not reflect all of that agent's preferences, it can reflect something narrower like "that agent's preferences excluding preferences that refer to other agents and which those agents would choose to veto". (Of course, that's a terrible hack, which must be added to the hacks to deal with varying population sizes, divergence, and so on, and the resulting theory ends up being extremely inelegant.)
In You Provably Can't Trust Yourself, Eliezer tried to figured out why his audience didn't understand his meta-ethics sequence even after they had followed him through philosophy of language and quantum physics. Meta-ethics is my specialty, and I can't figure out what Eliezer's meta-ethical position is. And at least at this point, professionals like Robin Hanson and Toby Ord couldn't figure it out, either.
Part of the problem is that because Eliezer has gotten little value from professional philosophy, he writes about morality in a highly idiosyncratic way, using terms that would require reading hundreds of posts to understand. I might understand Eliezer's meta-ethics better if he would just cough up his positions on standard meta-ethical debates like cognitivism, motivation, the sources of normativity, moral epistemology, and so on. Nick Beckstead recently told me he thinks Eliezer's meta-ethical views are similar to those of Michael Smith, but I'm not seeing it.
If you think you can help me (and others) understand Eliezer's meta-ethical theory, please leave a comment!
Update: This comment by Richard Chappell made sense of Eliezer's meta-ethics for me.