I like your overview and relation building (the main interface) and I think Napkin could end up being my most efficient way of collecting fleeting notes and doing the first low-level sorting/processing for later integration into my personal knowledge management (PKM) system, which is currently built using Concept maps (I use VUE https://vue.tufts.edu ).
I am tinkering with Obsidian, which is better for longer texts. Obsidian graphs are not so strong as your approach as you have to build the relationship by hand. That said, I don't think you should spend your energy trying to match the editing and markdown of Obsidian and the gazillion other notetaking apps that exist. I doubt you will be able to compete with the other systems. Instead, I would recommend that you focus on the "fleeting notes" capture, magic labeling and initial sorting into stacks. With this in mind, your stacks are excellent for this, but "copy to clipboard" doesn't quite cut it for me. I need better ways to export notes from Napkin to other systems. Preferably an API call that could spit out the export json for a stack or a list of stacks. With this, I could write a script or maybe even an Obsidian plugin that would pull new notes from a stack into my Obsidian vaults.
In short, my PKM workflow would be as follows:
Napkin for capturing fleeting notes - either directly or using Microsoft Office lens.
Napkin for discovery and basic organization into stacks.
Obsidian plugin or a python script to regularly pull new notes from Napkin.
Obsidian for text-heavy PKM and note taking.
VUE for structure and associative knowledge with linking to Obsidian for detailed and nicely formatted permanent notes.
Sorry for the long post - I just wanted to give you the context and motivation for my request :-)