That's a fairly weak argument: you can browse an electronic document in a non-linear fashion way easier than a book.
And also: books don't have CTRL-F
How do I make handwritten side notes? How can I create a bookmark for a specific page? How can I view multiple non-contiguous pages next to each other? How can I reference a specific part in an electronic text (in non-electronic text "3rd paragraph on page 11") and send it to a collaborator?
However, to nevertheless address your points:
>How do I make handwritten side notes
There is a number of applications to do this (e.g. xournal), and when combined with a touchscreen on a decent hirez modern device, we're getting close to what paper can do. I'll grant you: this is still the weak point of computers as compared to pen and paper (especially for scribbling diagrams), but it won't be for long.
>How can I create a bookmark for a specific page
I'm not sure if you're trolling here, all e-book readers I've used have this feature.
>How can I view multiple non-contiguous pages next to each other?
Multiple windows ? CTRL+N ?
>How can I reference a specific part in an electronic text (in non-electronic text "3rd paragraph on page 11") and send it to a collaborator?
Cut and paste?
Or ... sending him an email with ""3rd paragraph on page 11"" in the body?
If you present a 100 page book as a folder of 100 image files instead, most of these become image manipulation problems:
>How do I make handwritten side notes?
The same way you'd edit an image.
> How can I create a bookmark for a specific page?
Create a subdirectory with the page or a link to the page.
> How can I reference a specific part in an electronic text (in non-electronic text "3rd paragraph on page 11")
Cut and paste the excerpt into a new image file.
> and send it to a collaborator?
File sharing is a solved problem. Hell, you can even share it on Instagram if you so choose.
1) Mathematicians write all over the papers and books they read. Electronic versions of this exist (e.g., Xournal, written by a well known mathematician), but they tend not to be as convenient as simply scribbling on paper.
2) Mathematicians digest papers nonlinearly. Digital presentations don't usually lend themselves to flipping back and forth between pages. At times, I suspect mathematicians use papers and books as memory mansions, organizing concepts by relating them to their location in the physical copy.