That being said, I wouldn't trade typing on a computer for writing on paper, given the sheer speed I can achieve with one. But if we're limiting ourselves to trying to better increase retention and understanding, then I think pen-on-paper is the most valuable thing one can do.
Each iteration of formatting hopefully progresses the display of the information towards its ideal. You know when it's worked (and when something isn't working out and you need to quit and try something else).
To me the benefit of writing is that it makes me deliberately make a decision as to what I transcribe and what I leave out. If I skim read I often find my mind has drifted and I need to turn back some pages. Also, writing takes effort. If you notice you keep writing the same word/phrase, you'll give it an acronym. If you find repetition of concept, maybe you'll just draw an arrow pointing back to the paragraph the concept first came up - and your longhand is starting to turn into the next iteration already.
I remember doing python the hard way years ago, which encouraged you to type in the example python programs and run them yourself. It made a definite difference to sort of deliberately slow down and absorb during the exercise.
If I grow old & senile some day, I'll forget how to wipe my ass before the last Z80 mnemonic slips from my mind.