I don't read most of that the way you've read it. For example, Yvain said "Saying that there are likely flaws in mainstream medical research doesn't license you to discount any specific medical finding unless you have particular reason to believe that finding is false." Discount is much stronger language than simply reducing weight in the claim.

It's not clear what Yvain indented to mean by "discount"; however, the rest of his argument assumes he can disregard the base rate unless there you have specific evidence.