I do understand your point. I bought MarginNote for the reason that it supports various document types (incl. epub, as advertised) and allows to combine and organize excerpts in one space. Some books, even in the academic world, have become only available in epub format, besides a print version. Especially in the realm of psychology.
In addition to academic use I wanted to use MarginNote to allow me to take notes on non-fiction books. I initially planned to append a new book I’m reading to the topic-specific space in MarginNote and group information from various sources.
Right now it is such an unpleasant experience.
I personally do not want MarginNote to become a fully fledged ebook reader app. It would be amazing though, if highlights from Apple Books could be imported to MarginNote. Even if this would only work on macOS.