Livio, you are articulating a well-accepted position, but there are flaws in your foundation.
A printed page made for a reader with no relevant disabilities is a random-access medium. You can look anywhere you want and read anything you want in any order, or just put the book on the floor and admire a double-page spread.
Electronically, the issue becomes reading order (“logical” reading order in the terminology). Do the contents, when read start to finish, make sense? If you jump in at a certain point and read _from there_ to the finish, does it make sense?
In InDesign, proper threading order of text frames results in (e.g.) a tagged PDF with a logical reading order. It is true that the designer must make a decision as to when the reader is to experience a callout or a sidebar. My experience is this is only occasionally a real cause for debate.
The same applies to actual E-books. You need a logical reading order. ePub allows CSS placement of callouts and sidebars, which could instead (or in addition) be separate files.
Not every aspect of print graphic design can be duplicated in electronic document design, which relies fundamentally on structure, not inferences drawn from appearance.