While I'm not a professional typographer, I currently work in user experience, so I might have an answer.

From a cursory glance at the CSS, it's solid black text on a solid white background. This can have slightly too much contrast, which can become tiring to read. Off-black text on an off-white background tends to help I find. Apparently this effect is even worse for dyslexics, and "not-white" is specifically mentioned in: http://www.bdadyslexia.org.uk/about-dyslexia/further-informa...

black on white, links not underlined, letter spacing and uppercase in links wrong, line-height / parapgraph spacing ratio wrong (this one's most important and making it all ugly IMO), two column index - that one's really cruel, uppercase / lowercase first letter mess all around.

the page definitely looks a lot better with CSS disabled.

Yup, I immediately did View -> Page Style -> No Style and was surprised to find links!

Very low information density (huge fonts). Nothing actionable over the fold on the start page. Don't know what is actionable after scrolling because no highlight of links etc. Navigation is on the bottom so you have to scroll all the way down even if you just browsing through. No way to quickly navigate between sections/chapters from the navigation menu.

Typography and content aside using it feels like a book, but not in the good way.

I agree. I get the feeling it would look great on print. On screen it looks strange. For me zooming out helped.