This is quite doable now at least with PCBnew. I agree that repository layout leaves much to be desired, but scripts do help. The eeSchema is a pain though. The default behavior of scanning libraries every time when opening existing project does cause issues when symbols in libraries change. You can put cache at the top of the library list, but you have to do this each time you create new project.
I can imagine that eeSchema could be patched to do this automatically on project create. But I doubt any dev would start with this since bigger changes are in schedule if I am informed correctly. The patch would:
* make current rescue dialog redundant
* would also make eeSchema and PCBnew act consistently on the same issue (PCBnew has internal cache and looks first in cache, then in the libraries)
* would remove any issues with library consistency for old projects
At this point the most that can be done is to setup proper example and documentation for both approaches.
As for the future I can only agree with you
It makes no sense to implement and maintain new feature, that is freely available and maintained. It is not like there is a plethora of developers available for KiCad.