I can't speak for others, but I prefer a list of changes, so I can modify my source files and propagate to other versions. But I'm also OK with a modified ePub if the changes are only the corrections needed, so I can easily find them with a diff (i.e., no other changes in markup, file naming, structure...)
Regarding the missing hyphen, I'd recommend modifying the font with FontForge (if the license allows embedding in ePub, it probably also allows modification, but it might require a name change). It shouldn't be too hard to add a passable hyphen.
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