Indeed, EPUB3 provides all the features that the author wishes. His "portable EPUB" format is just a loosely specified subset. It's unclear if some extra featur

Indeed, EPUB3 provides all the features that the author wishes. His "portable EPUB" format is just a loosely specified subset. It's unclear if some extra features are included in the format as they are in his "Bene" tool, like the rendering of references (i.e. links with a data-target attribute). The EPUB3 standard is much more complex than EPUB2 (media overlays, mixing fixed layout with reflowed, MathML…). In my experience the implementations are much more varying, and most of them aren't complete. So a "Portable EPUB" may not render as expected because the reader tool lacks some specific feature. The author also requires full JS support, which I supose does not help with portability.