@drMerry - I understood what you meant perfectly fine, it doesn't change my mind about it
You *cannot* make two ePubs *binary* equal for the Find Duplicates plugin by manipulating them with a plugin like this. They will have different timestamps on the files for a start, which means Find Duplicates will report them as different, no matter whether the text inside is the same or not. So you are still going to have to run some other tool (like WinMerge) to compare them if you are going down that route. As I said above, I see it as too niche a requirement to justify the effort. However I know you have dabbled with writing plugins yourself, so feel free to create one for your own needs.
As for covers, it may be clear to you but sadly very fuzzy to me
. For an ePub when you send an ePub to your device or save to disk, Calibre is going to overwrite your cover with whatever your cover is that you store in your library if it can identify it, in exactly the same circumstances that clicking on "Update Metadata" will with this plugin. All the update metadata does is satisfy the desire of some users to do this step in advance for OCD reasons when they use the Calibre viewer directly. So I don't understand all your big cover, small cover comments or where you are trying to save space.