EPUB has a lot of features. A lot. I don't think anything (except maybe Adobe Digital Edition) support everything. I actually just realised yesterday that Moon Reader+, one of the best epub reader for Android, doesn't support vertical-rl layout (mostly used in Japanese book).
Even Kobo doesn't use EPUB as-is. Its native format is KEPUB, which has tons of id-tagged <span> inside the content. Moreover, KEPUB and EPUB on Kobo use different renderer (EPUB use RMSDK, KEPUB use Kobo's own) with different supported features. Isn't this a mess?
The new KFX format has one major advantage over EPUB. The images can be stored out-of-band. This allows you to start reading image-heavy book quickly, while images continue to load in the background. For fixed layout magazine/comic/manga where the entire file can be 100MB or more, this helps a lot.