The other reason to convert to the same format is to strip out bloat. The Tor.com bi-monthly short story newsletters routinely download as 20 Mb ePub files. Running an ePub-to-ePub conversions gets the file size to under 1 MB.
I tend not to fiddle around with the settings, but I know others do. I might do so if there's some dodgy formatting like bad hyphenation, but I'm just happy to have a readable file at the end of the day to load onto my Kobo.
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