The default settings for the Modify EPUB plugin is everything unchecked, pretty sure its been ever thus. It also ships with a help file, there's a link at the top right corner of the configure dialogue - the usage of the Manifest settings etc are explained in it.
There are � sequences sprinkled through the help file. My guess is that they're butchered HTML markup, possibly font related. Perhaps someone knows what they should be.
BR
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