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.
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?