I only mentioned Similar Stories because I knew it was content based, I've never used it nor did I write it so sorry to hear it does not suit what you need.
Find Duplicates has always had two very intentional limits placed on its scope - first that it does not compare content, and second that it does not limit itself to a particular format. Comparing content across your library (as it sounds like Similar Stories does) is as you know an exceptionally slow operation and not at all appropriate to this plugin, neither is doing an epub specific comparison which is what you are after.
For the majority of users, books will be identified by some aspect of their metadata as being duplicates. I have repeated ad infinitum in this thread that how a user chooses to "resolve" those duplicates is outside of what this plugin covers. The decision to merge, delete, or indeed more complexly binary compare contents of identified "duplicates" is all in the realm of either existing features of calibre or potentially new plugins for other users to write. I would suggest the latter if such a feature is important enough for you to justify the effort. Personally I have absolutely no use for it which is another reason why I have no interest in spending hours trying to craft it, and equally as explained above I do not see it as being an appropriate feature of this plugin. There is never any harm in asking or suggesting a new feature, but as always I reserve the right to say no to ones I don't think fit well
Good luck with whatever solution you pursue.