Because for its entire existence, the top HN comment on articles is typically a contrarian take or pointing out flaws. This goes double for a study, where people just hunt for some aspect of the methodology they dislike. If you don't address the flaws, then it looks like you never considered them, and the top comment will say that your entire methodology is suspect. It's super predictable to the point that you can harness this kind of reaction to get stuff on the frontpage if you really want to.