How do you add a book to multiple iBook collections? I'd like to organize my books into different collections and have a "completed" collection for books to be entered into upon their completion.

The problem is that it seems iBooks will allow a book to exist in only one collection, meaning putting it into "completed" takes it out of the other collection.

It also doesn't seem to allow users to add duplicate books. All of my books are DRM-free .epubs -- I could potentially put PDF versions of them into "completed".

What's your advice on achieving this workflow with iBooks and iCloud syncing?
There is simply no way to do this tagging on iOS 8 or lower. You are correct about the inability to have a book in more than one collection. 

I don't see forking a second copy of a book to have it in the completed category as well as a second one. 

My best advice would to be use a spreadsheet (numbers) to track completed status or some other third party note app or list manager. 

Perhaps look into Things by Cultured Code which is free this week in the US store. It makes lists amazingly powerful to manage and curate.