Is http://arxiv.org/pdf/hep-th/9907164v2.pdf#page=30 a reasonable approximation? It works in Chrome and should work with the Adobe plugin, but doesn't work in Safari. I don't know if PDF has finer scale references than page.
I dont know what is Adobe plugin. I will investigate.
However, just based on its name, I would probably recommend removing it. The combination of these two words, ``Adobe'' and ``plugin'', makes me feeling uneasy :)
Which brings us to the second point: there is no good open-source PDF viewer. If you care about using open source, then go HTML.
Also, if they submit a revised version, it will be a different page. Anyway, I don't think we will ever get a good PDF reader, because there is no demand. People read HTML.
After a little more digging, I've found that pdf files can have named destinations, like eqrefs, so you don't have to use page numbers as references. See http://www.tug.org/pipermail/pdftex/2007-October/007383.html for how to make them in LaTeX.
This does require whoever generates the pdf to include the labels, but then so does html. It shouldn't be too hard to generate a reference to any named equation in a file.
What exactly is your problem with current PDF readers? PDF.js is pretty nice for browsers, Preview.app is standard on OS X, Linux has several that were fine and I know that Windows has many that are considered good alternatives to Acrobat Reader. Even phones and tablets do a good job, though e-readers do not.
I started that fork because I could not find a viewer which would keep vertical position, and jump back after following an internal link, and have bookmarks with charhints.
There is a conceptual problem, however: as I said, I feel that PDF is getting deprecated because of insufficient demand. If this is true, then it does not make much sense to invest effort into TeX + PDF. Maybe I am wrong.
Sometimes I think that I am simply allergic to TeX :)