Weasyprint does support all of these things actually, including footnotes. A table of contents would use references to CSS counters, and if you generate the input-HTML for weasyprint from pandoc, then pandoc can actually generate those for you. The only nontrivial thing on your list would be an index, assuming you would want to autogenerate it the way latex does, but even that seems kind of doable with a little bit of custom hacking. Pandoc can also do bibliographies through citeproc/csl. So pandoc+weasyprint is absolutely a practicable tech stack these days for science publishing, assuming you don't need latex-math and are not targeting any of those publishing outlets that give you a word template and latex style and force you to use it.