Agreed. A way I do it is to take a picture of a page, and then use my phone's image editor to add the annotation directly to the photo.
Prepare some strips of paper like this guy does, and make notes on them while reading. But then, also always take pictures of the page, with your strip of notes in the picture.
That would solve both of the problems he mentioned:
> The downside of this is that in order to annotations to make sense, it requires a physical copy of exact same book. Another one is that it doesn't have automatic timestamps, which somewhat bothers my #lifelogging OCD.
If you take a picture of the page and the strip of notes then you get the timestamp for free. And by including the page of text in the picture you have that context preserved as well.