I think if you reframe the problem it can be much easier (if not trivial) to find solutions.

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.