Just writing this up in case it helps anyone else because it wasn’t automatic.
Sync books onto.. and All booksShow this iPad when on Wi-Fi and Automatically sync when this iPad is connected
Did it not work syncing through iCloud or did you have reasons to avoid syncing through Apples services?
I have mainly ebooks but a few random PDFs and they sync through iCloud. However you need to enable it in the icloud settings rather than in the ibook app settings.
Which iCloud settings Hallski?
I am only shown these:
I have iCloud Drive off because:
iCloud Drive is automatically set up on any current Apple device running the latest operating system.
Apple’s macOS will automatically save files saved to your Desktop and Documents folders to iCloud
source: How Apple's iCloud Drive works — and how to use it | Computerworld
I don’t want any of my personal files on Apple’s (or anyone else’s) servers (unless those above such as contacts etc)
Ah, on the Mac it seems to be in Books->Settings->General: “Sync collections, bookmarks and highlights across devices”.
On iOS there seem to be a setting in both iCloud and inside the books settings, to be honest I don’t know how they interact. I have both enabled.
With regards to iCloud Drive and Desktop & Documents you can disable those:
I see the first option (sync) but how do you get to the second pic options? I know I’ve seen that screen before but can’t seem to find it now 
I am not getting that when I switch it on… and then when I try to turn it off I get:
So it looks like it wants to upload everything first and then let you choose? 
Maybe I am turning it off too quickly and need to give it at least 5 minutes first…
Edit: Duh I found it!
I was going to System Prefs > Apple ID
But you need to go to System Prefs > Internet Accounts for the Options to show
Thanks Hallski!
I was actually in System Prefs > Apple ID but maybe it is different after it’s done syncing? 
I reformatted my Mac and wanted to sync some books and ran into the same issue.
This time I just did what you suggested - iCloud > iCloud Drive > Books enabled (and the equivalent on my iOS devices) but when I double click an ePub file, it opens in Books, but it does not then automatically transfer to my iPad or iPhone 
What I have to do instead is Airdrop the epub file on to the iPad. Once it’s on the iPad the syncing of highlights etc work fine - so if I highlight a paragraph on the iPad it will show highlighted on the book on the Mac (and from Mac to iPad). But it doesn’t seem to automatically copy the books onto the other devices, is that how it works for you too @Hallski?
(I would have thought that just opening a file in the Books app on any device would automatically copy it to others synced vis iCloud)
Terribly sorry for the slow response. I saw your question and then forgot about it. I just tried to add a PDF to Books on the mac and it showed up automatically on my iPhone within seconds.
I simply dragged the PDF into Books on the Mac. If I then clicked the “…” menu and choose “Remove” I got a question if I wanted to remove it from all devices.
Yes, in fact that is what I have been using the most.
That’s definitely epubs you’re dragging on to it and not epubs you’re buying from the books store right?
It’s still not working for me… I wonder if I have Little Snitch blocking it (I think I’ve blocked a few connections originating from Apple services going to google or aws. I’ll have to check.)
Yes, bought from Pragprog and dragged into the app. 
Thanks @Hallski - I’ve got a call with Apple Support tomorrow, maybe they’ll be able to get to the bottom of it. I’ll update the thread if there’s anything to report 
Good luck! 
I’ve just been on to the phone to them for the last few hours and unfortunately everything they suggested did not work. However just as they were about to escalate things to an engineer I thought I would uninstall Little Snitch to see if that helped (previously I had disabled network filter while troubleshooting) so I uninstalled it, tried again but no joy 
But then I installed it again, and also logged out of iCloud and back in again. Well this time Little Snitch asked me to allow Cloudd to connect to Google’s servers (I know for a fact that last time I clicked deny) so this time I clicked allow… and it all works now! I now need to simply open an epub in Books on my Mac and it automatically transfers to all my iOS devices 
So here’s what I think happened:
Then logging out of iCloud and back in again re-triggered the connection which re-triggered the request in Little Snitch.
I’m just glad it’s all working now! 
Thanks for your help @Hallski - if it wasn’t for you I might have thought I had to keep connecting my devices via cable or airdropping to transfer them over!
Yay, success!
Really glad you got it sorted in the end. 
Me too @Hallski!
For anyone who runs into similar in future, this is the connection you have to allow:
