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3.1 and 3.2 are both intended for generated temporary files (txt/html) -- save only at your own risk, and not into ePub!
My notion for 2.3 would be to merge from <body> to </body> (tags excluded!) and put into an <html><body> ... </body></html> container: option save to "plain html" -- never ePub.
As a matter of fact, I cannot conceive of an ePub Merge tool which would work ... maybe somebody else can??
My notion only for ePub diff -- and maybe save bits for further editing with a dedicated tool.
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