These factors are influenced by material constraints and opportunities, but don't discount the importance of design iteration in the simplest of objects.
And as someone who has spent a lot of time drawing, the feel and quality of different pencils (wood, graphite hardness etc.) is something people care an awful lot about.
In that sense most software today isn't a pencil. It is more like a fully furbished office where you are not allowed to use a pencil but you have to use a silly oversized rubber-ballpen with decorative feathers instead. Oh and the paper is made of plastic and you are not allowed to change it because the guy at the door will beat you with a stick. On the bright side the filing cabinet might be the best you have ever seen — but you really aren't enjoying it all that much because you feel forced to write on plastic with a goofy pen that changes colours every 4 months. Ah, and you are forbidden to take the plastic writings out of the room (again the man with the stick).
I cannot believe that it is 2020 and the best thing we came up with is still just a text based shell (nothing against those, they are great, but I'd love to see the same modularity in typical GUI applications).
https://www.thearchitectsguide.com/articles/best-smart-pen
(#7 includes saving to Slack)
To attempt to parallel the ergonomics of a pencil, good or otherwise, with some grand UX narrative feels inappropriate. If the 'interaction of graphite on paper' is to your liking that is very much an accident of design rather than a result of any pencil designer's intention. 3b, HB, or 3H madam? Methinks that the primary driver of the pencil factory of both yesteryear and today would be maximisation of production vs units of wood, lead, or rubber. The 'way it falls on your fingers' a consequence of resource constraints nothing more.
The experience of writing with a pencil is perhaps the better for not being messed with.
The pencil survives and has survived by being always useful, value for money, and fit for purpose.
Model those attributes and users will accommodate and grow to love your products UX regardless of its failings.