It doesn't mean that, no.
But it does mean that I ought not behave as though objective, scientific facts exist until I have some grounds for doing so, and that "some people think their intuitions reflect objective, scientific facts" doesn't qualify as a ground for doing so.
At this point, one could ask "well, OK, what qualifies as a ground for behaving as though objective, scientific facts exist?" and the conversation can progress in a vaguely sensible direction.
I would similarly ask (popping your metaphorical stack) "what qualifies as a ground for behaving as though objective moral facts exist?" and refrain from behaving as though they do until some such ground is demonstrated.
I don't think you're in a position to do that unless you can actually solve the problem of grounding scientific objectivity without incurring Munchausen's trilemma. That is essentially an unsolved problem. Analytical philosophy, LW, and various other groups sidestep it by getting together with people who share the same intuitions. But that is not exactly the epistemic high ground.
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: