Most of the pdfs I read that have tocs are dead text and give references in units, be they page numbers or chapter or section numbers, that bear no relationship to the actual pages as displayed in the bookmark section.

I personally believe that as an old time LaTeX aficionado I should beg to differ. I find that most documents compiled with hyperref and either the standard classes or memoir.cls (and surely the Koma ones as well, although I have no experience with them) come out with all sorts of appropriate hyperlinks in the toc and elsewhere. Of course, like anything else in LaTeX, one may have to fiddle with some setting to fine tune the appearance of them and some other details. In this sense, most articles on arXiv are also duly hyperlinked.