A fork of Godot optimized for native apps would be a good idea. Especially if it learned the lessons of the web stack and used basic text-based formats for describing layout and theming (like HTML and CSS). Maybe something like QT. Something simple, flexible and portable that's as easy to use as Electron but doesn't require lugging around a 60mb Chromium instance for every application.

Some work would need to be done improving text rendering, layout and to add more GUI elements. Probably a lot of stuff removed from the backend that isn't necessary (apps won't need physics or lighting, probably.)

I made a basic theme loader for a project ages ago based on the config file format because dealing with theming and fonts was a pain at the time. Nothing novel, it was just a dictionary that had node paths as keys and set values. It is possible, I don't know why Godot makes some things more complicated than they need to be.