You're confusing the language with the build system. LaTeX wouldn't be very useful without the awesome build system. This project is a build system for producing both high-quality HTML and high-quality PDF (through latex) with a single, high-level ReST markup language. It also uses latex formulas for math.
The HTML format does generate multiple pages for different sections and chapters, completely configurable. The format above is the singlehtml format where everything is on one page. I'd much rather have a link to a specific anchor tag on a page that goes directly to where I want than a citation to a page number on a 200 page document.
Agreed, but for my case, I didn't really care too much about the PDF output. The printed version of my thesis is going to sit in my university library untouched forever. I'm much more concerned with having a semantically correct, searchable, beautiful HTML output.
Yeah, my university formatting requirements are crazy also. This allowed me to have one source that outputs (nicely) to a bunch of different formats, including the university PDF requirement.