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.
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.