How do you add a book to multiple iBook collections?
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.