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I think I have the cause, for myself and op, and others.
According to notes from a few iBooks compatible readers it appears Books stores and transfers the ePub files exploded. When a book is dragged out of the app or transferred out it is again compressed.
Apparently the compression order remains the same for the iBook format, not ePub.
Reviewing the LZ log shows the order of operation.
Clearly Apple has no intention of fixing this. The problem dates back many years.
The solution must be taking on of the few open source options and adding it to a popular conversion program, eg Calibre.
eCan is open source. So the solution would be to create an import filter.
I also found my problem with ECC; path length. Pointing to a folder one deep solves the problem for most documents; giving near 100% action.
This situation does explain how some books can be many times larger on the iPhone or iPad than the source file. Already large technical manuals can take up hundreds of megs of space expanded.
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