Since in Bukkit-based implementations all worlds have to be in the WorldContainer (which is the server-directory by default), it would be reasonable to make the world paths in the render.conf relative to that instead of the server-directory.

This will be a config-breaking change so it should be implemented together with more breaking changes.

This will not be implemented.

Most of world-loading and rendering is done with platform-independent code (BlueMapCore/BlueMapCommon) which also resolves and loads the worlds based on their path on the file-system ... This is always relative to the working directory.
Moving the base for the world-folders away from the working-directory only for one implementation (Spigot) would break a lot of things and create a ton of issues. It would make things more confusing and I believe the cleaner way is to look at the worlds from bluemaps perspective (working-directory) and not from spigots perspective (Bukkit.getWorldContainer()).