An option box is a good idea, both intuitive and non-obtrusive. Widening the GUI itself is also a good idea, I can see it go both ways.
To me, the GUI we have at the moment is quite minimal in contrast to how custom each publish could potentially become. I can see it grow into a much more capable GUI, more akin to an actual editor as opposed to just simply visualising data.
However, the issue I see with extending the GUI is that it is simply a hard thing to do. Personally, both QML and Lite are at the tip of my knowledge in user interface development. I believe we need a more efficient foundation to add more interactivity and features to either, something I'm simply not familiar with.
Having @mattiaslagergren onboard could propel things in this direction, but I am uncertain with how familiar you are with this level of complexity in desktop-land? It could potentially be built with web application tools, like Electron, similar to how QML is a client/server-type application.
I would ideally take someone on with experience in editor-style GUI development. Someone who could potentially consult in an appropriate direction and set guidelines for how to technically build up to a high enough level, without introducing brittleness. Also here, with @mattiaslagergren and c/o, that could potentially be possible.
Without assuming much, the most realistic option to me is the option-box approach. That is, many small GUIs working together, as opposed to one capable GUI, even though I'd personally prefer the latter.