The JS is only added if the reference KePub is in place, so that's considered optional for everyone. It may improve the experience but is not required. Similarly for style hacks, it improves the experience but isn't required. There are no special divs, only spans. The kte file is indeed for troubleshooting only, it encodes some data about calibre and plugin versions, selected options, and the date and time of conversion. It should always be added but other than me needing more information for troubleshooting it's OK to be missing.
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