Welcome to the MarginNote forum! It’s good to have your inpu here.
It’s not an issue of PDF vs epub. The ePub experience doesn’t lack features available to PDFs as far as I can tell (except for bookmarks, oddly enough). It’s more of an issue of MN not taking advantage of ePub’s features. ePubs can do things that PDFs never can because ePub is based on HTML. It’s dynamic, it’s pliable. By contrast PDF is merely a digital photocopy. Epub doesn’t require much to give you a word count, a page count, to edit metadata.
Here are some example of screenshots I took using another epub reader.
Most puzzling is that MN won’t render the files in the format they are encoded in, i.e. the “Publisher’s layout”.
In the image above, the original Publisher’s format is seen at top left. But you can change it to look however you want. Below are some of the things you can change in an epub with little effort in some apps:
Now imagine that with the powerful annotations of MarginNote; a sidebar, importing images into notes, etc. It would be unstoppable!