We have some internal plans to improve the ability to document things - not just a markdown-ey resource file, but perhaps some ability to render those markdown files out into a static webpage to semi-automatically generate an entire reference manual for your project.
I don't think you can do things at the level required from a third party module; it would have to be a first-party integration to hook in to these context menus everywhere. If I remember right, the Documentation tool works the way it currently does as a stopgap; adding a readme.md to every resource might require adjusting the logic for how each workspace saves & loads resources, which made it a bit of a harder sell at that time.