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I read on an e-ink device, and when I get ebooks incompatible formats, including most PDFs, I convert them first. I'm not in the main buying group for that trait, but I'm not an extreme outlier either; a lot of people throw everything they buy into Calibre to manage their collection, and export-to-device in whatever format works best for them.
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You should remember that to the average user, calibre refers to the ammunition they use in their guns, not software

I think you may be overestimating the technical challenges here: advertisers have ALWAYS tailored their ads to different formats and devices. There are different AT&T ads for TVs, magazines and the Web.Its what advertisers DO.
Meanwhile, I'm leafing through my high-toned literary magazine(The Atlantic) and I'm seeing ads before, after, and in the middle of long-form articles about presidential politics and other Very Important Topics.
Again, you might be right: maybe book buyers will absolutely not tolerate ads in books , other than splash ads at the beginning and the end. However, the KSO example indicates that even THAT may be significant. There were plenty of people here and elsewhere on the Interwebs who said that $25 off for tthe KSO would not be enough to spur sales of the KSO. Well, they were wrong.
There are lots of games that go for $0.00 ad-supported and $4.99 for the premium no -ads upgrade. Ditto software. I think ebooks could also work. Those squeamish about ads could just pay full price right up front
Meanwhile, this is being tried
HERE, where they are doing both freemium and subscription. We will soon see what works.