No I wouldn't put it in the Find Duplicates plugin either.
It is a very niche requirement imho. I reckon most users take the same approach as myself of just eyeballing two formats that are the same, by looking at them in the Calibre viewer. I believe I can far more quickly tell which version I want to keep by skimming though a few pages that trying to interpret WinMerge results. For many situations the slightest change (like a calibre style being renumbered) is going to show every single file as being different but may have no impact on the result. Any edit in Sigil is going to reformat the contents or put other filth like ids and inline styles. There are too may reasons why a merge type comparison has little value imo.
But I don't want to turn this thread into a big debate about it, because regardless of whether you agree with how useful or niche it is, I'm afraid I don't see it applying to any of my plugins.
If you can write javascript, you can write a Calibre plugin in Python yourself. I had never written a line of Python in my life before I developed the plugins in this forum, and the other developers have been very generous with their time in helping when you get stuck (keep any questions very specific of course).