I think ePub's can handle everything you mentioned, ePub's are just XHTML, and a subset of css [1]. Not sure about callout boxes, I don't know exactly what subset of elements are available as I've never written one, but everything else you've mentioned looks to be available [2].
Fun epub file trick: rename the file .zip, unzip -a yourbook.zip (double click unzip doesn't work on osx for me for some reason) and check out the html, css, images and xml of your book.
There's actually quite a lot of evidence that it was a politically motivated spear phishing campaign from FancyBears, which is most likely from Russia. So technically yes there's no definitive, smoking gun proof but "no proof for this claim" seems to be a bit dismissive of some glaring hints. It certainly wasn't just a "generic phishing page" or guessing of a weak password.
They went after quite a few politicians on both sides of the aisle and journalist's, the Podesta camp just happened to be the ones who fell for it.
Fun epub file trick: rename the file .zip, unzip -a yourbook.zip (double click unzip doesn't work on osx for me for some reason) and check out the html, css, images and xml of your book.
[1] https://en.wikipedia.org/wiki/EPUB [2] https://www.w3.org/TR/2005/WD-xhtml2-20050527/elements.html