It is very frustrating the number of people who say "it's their property, they can do whatever they want" and similar comments, all of which are missing the point. Yes. It is legal to write on your own property. I know thay. It's my opinion that they're doing something that is guaranteed to harm overall human knowledge: whoever purchases/inherits/digitzes the book has to deal with it. And it almost certainly harms their own understanding of the book.
If by that you meant to suggest that for formal study, some kind of self-review process combined with cold written practice/rehearsal sustained under interleaved spacing, then that is likely the gold standard for comprehension and memorization. But most people don't even know that, either.
But the main premise is we should not assume all book reading is for rigorous self study. Margin notes can be useful for other purposes than direct understanding/retention (I admittedly don't know the psychology evidence for it but many academics routinely write margin notes here and there on (poorly written/edited) papers for purposes of idea generation, scientific criticism, etc. Presumably the Edison example mentioned above would have been more like that.).
A book with notes is a guarantee that the book didn't spend its life sitting on a bookshelf not being read. If people are reading it is a net positive for overall human knowledge.
Lastly, your usage of Socratic teachings is a hollow appeal to authority. Socrates is dead and a modest library in an elementary school would surely have brought him to tears had he known how far we've come as a species, much less the remainder of books currently available.