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Are Physical Interfaces Superior to Virtual Ones?

Something's been bothering me ever since I started reading books, especially non-fiction, on my Kindle:

I can't remember where anything is. Physical books are full of spatial reference points; an especially beloved book is a physical topography in which we develop a vague sense of which chapters contain relevant information; even where, on a page, a particularly striking sentence or diagram lies.

Ebooks have none of these referents. They're searchable (or at least, some are) which mitigates this issue somewhat. But I'm unlikely to remember that a fact was at "41% through a book" for one simple reason: my hands never got a chance to find out what 41% through a particular ebook feels like.

The entire article is very interesting, but these paragraphs in particular caught my eye - finally, an articulation of one of the main reasons I find myself dissatisfied when reading in any kind of digital format.