IBooks and scrambled ebooks, original ebooks deleted

It seems to me that iBooks on Mavericks gives you some massive disadvantages.
iBooks from the files from
.../Music/iTunes/Books
to
.../Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/Books
On this process
- all names are scrambled in the new location, possibly the files themselves as well
- original files are deleted with no notice
Does anyone know more about the process? Are the files scrambled or inflicted with DRM?
Can anyone suggest a good ebooks reader as an alternative to iBooks?

I have done this and I too would like to know if I can transfer some of the books that don't show up on my iPhone to iBooks (on my iPhone).
Anyone have an answer for this yet?

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