Hard agree on highlighting. I never understood it. Well highlighting and also the post-it notes marking of pages. It's just too much. Never worked for me. I only did it when I was forced to by teachers!
But not for the reasons you're stating. It was just more like "unreadable". There would've been essentially a post-it note on every single page. Or I'd highlight like half the page.
It's a bit like bookmarks in browser for me. I started out trying it. Neatly categorizing things in a hierarchy. It just doesn't scale. And I see people like your parent, with elaborate systems of bookmarks and they navigate the hierarchy, failing to find what they need, often giving up on it in the moment, saying they'll "find it later". Dude, guess what we're in a call together right now discussing a topic, either you find it now or never!
On the other hand, I don't bookmark anything at all any longer. But I'd die if I lost my history ;)
As in, I somehow remember the terms to write to find what I need and the browser finds it in the location bar history (made up of actual browser history and bookmarks if I had any of course) but it also applies recency/number of times I used it (I never bothered to look at which of these they actually apply). But I just know all I need to type is `n` and hit enter and based on how often I come here, that's gonna get me to hackernews!
Similarly at work, I remember phrases, parts of ticket summaries or even just the current epic everyone's talking about and I type in the number/summary parts and find what I need.
I could probably spend hours "organizing my bookmarks" (i.e. post-it notes and annotations) but I don't. Never needed it, never made sense, never worked. But it does need to be digital. I'd die if I had to be a 50 years ago librarian!
---
On the actual article though: writing by hand definitely is awesome in general. Learning other languages in school we had to learn the vocabulary by writing translations of terms into books. Often I could tell you that "this is the third word on the second page" but not the actual translation :)