I've had some success using the Kindle app highlight feature - highlighting key points as I go along, and then later reviewing just my highlights (which can also be exported). You can add notes to the highlights too.
I do this too using my remarkable (reader tablet )and then scripts that export highlights / notes which I then index for as plaintext - it makes this process much more seamless.
I use https://github.com/lucasrla/remarks, which OCRs (text recognition) your highlights to extract what exactly was highlighted, and also outputs screenshots of all pages on which I wrote notes.
This way I can go through my annotations sequentially, save highlights / their main ideas, and reformulate my notes into plaintext a bit more clearly.
This is just subjective, but I use it to read many books and enjoy it. I can scribble / highlight / notetake very easily and find the whole experience quite convenient.
Oh, I was just reading reviews (probably on reddit?), and that seemed to be a consistent opinion. It looks like a really cool device, but I've heard it's a little one-dimensional.
Edit: Looks like your link to the sibling comment is for extracting annotations from pdf. Are most of the books you're reading on remarkable in pdf format instead of epub?