Gwern makes it pretty clear that the objective is a minimalist aesthetic, not a minimalist design through-and-through.

Not to mention that the same paragraph specifies a design requirement of the site:

"What does it take to present complex, highly-referenced, link-intensive, long-form text online as effectively as possible, while conserving the reader’s time & attention?"

Even the minimalist answer to that question would probably feature the things you're objecting to.