Honestly it's very difficult to imagine a case where pen is better. I can type faster than I can write, and everyone can read my typing much more easily than my writing. Etherpad (sadly killed by google) had a great annotation UI. Maybe for serious mathematics with formulae, or something where you want to annotate 2D diagrams (architecture?), but that seems pretty niche.

I can, not saying you can’t, but technology using a pen interfacing with a computer is decades ok and mature but is still not commonly used hence I don’t think it’s a useful tool in general.