For me I think the distinction is more about structure and rigidity than keyboard vs pencil. Sketching free-form notes and especially little diagrams is a really powerful thinking tool. I also like to sketch my thoughts in org mode, which has some advantages over paper (structural editing, ability to zoom in and out by folding subtrees) and some disadvantages (tree structure instead of arbitrary spatial structure, more friction for diagrams).

I have a really hard time using WYSIWYG editors for thinking-by-writing. I think it’s because it’s hard to see partially-formed structure so it feels less malleable.

Yes, me too! I like using sketch notes to think through things nonlinearly, then I make an outline in Org or use an AI to get the text from a sketch, and then maybe I'll refine the sketch so it can be an illustration that I embed back into Org. Structural editing is fantastic for reordering thoughts and converting back and forth between lists and paragraphs/sentences.

but then, from personal experience, once you master, and practice photoshop/illustrator-like software, it becomes not so hard to actually produce quite complex visual communication in little to no effort. it is questionable whether I'd ever be able to do so with pen and paper, though, of course, the feeling... the touch of it is second to none. Talking of practicality though, it makes me wonder. I think rather an important question is whether we also talk about writing/note taking as part of larger personal information management system. It is very likely having one (such own KB) matters even more than the medium itself.

You can get the best of both worlds by picking up a Wacom tablet or similar. It isn't exactly the same, but it does then mean you can doodle but with the power of the capable software.