> That's the goal of Zuunote. And I hope it shows here through the way it implements links. But I'm way in over my head.

Markdown is well covered. Have you considered building on Scroll instead?

IMO, having used them now on thousands of pages for years, Scroll does links better using our "aftertext" pattern (https://breckyunits.com/aftertext.html):

https://try.scroll.pub/#scroll%0A%20%23%20Scroll%20Links%0A%...