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gwern comments on Help us Optimize the Contents of the Sequences eBook - Less Wrong
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You can embed arbitrary javascript in PDFs, so what about including "phone-home" text-boxes for marginalia in rather the same way that online editions of Real World Haskell and other programming books have comment threads for each paragraph? I'd think other metrics like time-on-page could be measured as well. This would need to be disclosed, of course, and not every reader can be expected to comment, but the "how" seems tractable at first impression.
I don't have any useful insights on what response to measure.
This doesn't seem usefully true. Some googling for search queries like 'a/b testing PDFs' or 'PDF phone home' show no one discussing the topic of A/B testing different versions of PDFs, and Wikipedia indicates that only Adobe supports JS and even it produces a popup when you try to phonehome. So any A/B test is going to work on only a fraction of users (how many LWers still use Adobe Acrobat to read PDFs?), and it will alarm the ones it does work on ('is this PDF spyware‽').
Foxit Reader supports javascript, and libpoppler (which powers evince and okular, among others) does as well.
Without something to measure, though, that's really just a technical curiosity.