Some of the exclusive features of printed books may be relevant for learning, perhaps the tactile sensation or the role that books still have in our culture.
I still find physical books are better when I want to master the whole content of a book.
An often overlooked physical aspect of books is that they "live" directly in the environment, unmediated by screens, icons or distractions. Their physical presence prompts me to read them.
Embarrassingly, I've bought e-books and later realized I forgot about them. They tend to disappear into the "virtual shelf" or some corner of a hard drive somewhere.
The spatial landmarks you mention make a big difference for me. Somehow being able to hold the whole book in my hands helps me build up a mental index of what the book contains. I don't experience the same thing with ebooks.
I solved that by buying an embarrassing number of Kindles -- I just leave one dedicated to a book as I'm reading it, and keep it in a convenient and obvious location. I have audiobooks on my iphone for the gym (using the Audible app), audiobooks on mp3 SD cards for my car, a Kindle by the bed, and have a DX, iPad, second computer for reading things which change more frequently.
4-6 Kindles and everything electronic is still a lot easier for me than storing books.
A sound argument is that ebooks provide less spatial landmarks, this kind of context seems to be important for increased retention. See: http://healthland.time.com/2012/03/14/do-e-books-impair-memo...
In this usability research (http://www.nngroup.com/articles/ipad-and-kindle-reading-spee...) they found that ebook reading was slower than print for both the kindle and Ipad, however they weren't able to differentiate those two.