This is an old thread, but perhaps this alternative reply is helpful for someone.
I use a different app for reading, avoiding Books altogether. I use Kybook 3 and it just lets me copy files directly to the app... probably other third party apps will work the same:
- plug the phone into the mac
- open the phone in the Finder
- click on the 'Files' tab (some apps appear below, including Kybook)
- use finder to copy epubs into the Kybook app
Or another way is to Airdrop to the phone, then share with the Kybook app. This normally works, the plug-in option above works best.