The Full Justification switch in iBooks is like cruise control on a car - it takes control away, while delivering a consistent experience (at least, in Apple's opinion).
The fact that the switch is on by default is similar to having Auto Brightness on by default, and then wondering why you can't adjust the brightness.
Suggestion: Add something in the front matter of the book saying something like "to enjoy this book as it was originally formatted, adjust your iBooks preferences ..."
Or, if your boss really wants things to look right when Full Justification is turned on, reformat your book so that everything is fully justified.
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