Fos most of the rest of his issues, I think Zed's problem is that he thinks there's one obvious answer, but lots of other people would disagree with his one answer. Python tends to be either very opinionated, or very agnostic. Where there's One Way To Do Things, that's what you must do; except where there's obvious disagreement in which case it doesn't bless a single answer.
API doc autogeneration; I can guarantee that if anyone came up with a default tool with default output such that "doctool module html_directory" was all you needed (and indeed people have) then there would be widespread, perfectly legitimate, disagreement on any number of choices in the design of it.
(Prsonally, I think API doc autogeneration is entirely pointless, and indeed fundamentally the Wrong Thing To Do for most Python libraries. When I come across pages of JavaDoc-ish API documentation, I groan internally and just look at the source instead.)