I already gave you a brief explanation. If you don't understand it well then better don't change it.
Learn what an overlay filesystem is and when it's used. Overlay filesystem - ArchWiki then compare this new knowledge with this file LibreELEC.tv/tmp-autoconfig.mount at libreelec-9.0-rr · 5schatten/LibreELEC.tv · GitHub and I hope you will understand why your changes are not really needed.
Wow, condescending, much
I understand you cannot write to /usr/... and I can see what you've done however I don't think that it's working correctly? I have placed my joypad .cfg files in ~/.config/retroarch/autoconfig and this should be overlaid into /usr/share/retroarch/autoconfig correct?
mount shows this:
none on /tmp/autoconfig type overlay (rw,relatime,lowerdir=/usr/share/retroarch/autoconfig,upperdir=/storage/.config/retroarch/autoconfig,workdir=/storage/.tmp/autoconfig-workdir)
Sorry if I'm failing to understand this however all I want is to be able to access the retroarch config files over samba...