I find for technical books, paper is far superior. The layout is much better for graphics/ equations, plus the traditional layout of a book (with some post it stickies) is optimized for easy navigation/ jumping back and forth.
One thing I miss about paper books is their three-dimensionality. If you are an experienced reader, knowing where you are in the thickness of a book is just as important for navigating the book as a whole as where you are in any given page. And I don't think the GUI bookmarks work quite as well as paper, personally.
Really, it is all about fractions of a second, but it adds up.
(Personally, I don't care about the aesthetics, feel and smell of the paper, blah blah, I just still think paper technical books win for .)
Being able to rapidly backtrack and sidetrack seems to be the critical issue; paper allows you to do this so easily with a thumb or other improvised bookmark. Hypertext and forward/back navigation and tabs seems like it would be perfect for this, but it doesn't quite work.
Learning effectively from a technical book has to be like lazily reading a detective novel -- you have to be willing to look at the ending. You do this before you're in a place to understand it, and then build up that foundation to the point where it supports what the end goal is going to be. Maybe it's a question of having a writer who can make this idea a first-class one, by repetition and backtracking in a forward direction; effectively first presenting page 8, then 4, then 2, then 1, then 2, then 8, then 2, then 3, then 1, then 4, or some similar scheme to allow the reader to shore up their understanding, while allowing them to skim through parts that seem boring or are too confusing, with the knowledge that they'll have another chance to review the material, without having to manually backtrack.
I have read textbooks with a lot of patience spending way more time per page, letting the content sink in, thinking about it, taking notes on the bitsy corners of the book etc. However, these days as a professional, when I read tech books, I could see myself rushing for facts, and "how-to"s instead of deeper reading. May be I'm getting older? Wiser? Falling into Attention Deficit Disorder? I don't know. But, I do know that if a tech book does "8,4,2,1,2,8,2,3,1,4" like you said, I'm lost at third step, finding something else where I can get my facts quick...
This is where interactive books could jump in and help keep the attention in place with more relevant information in view instead of needing repetition.
I remember Apple tried something with a free app called iBooks Author. I need to spend more time with it and see if I can make use of it for some tech stuff.
I also think an experienced reader can navigate more quickly (yes fraction of seconds) in a physical book than possible when you have to set bookmarks and use them in some drop down system.
I would love to see a human factors study comparing hyperlink eReader versus paper book.