I have tried that with a share out of the mergerfs mountpoint, but with the same result. Restart after 4 seconds
So that doesn't work, my config is on a totally separate independent drive and it works, yours works if it's on your system drive, so either you leave the config on the system drive or add another drive if possible.
What does work is you could create a share, let's say call it EmbyServer on your mergerfs, leave the config on the system drive during setup of the docker point that EmbyServer to /mnt/share3. Emby will then start inside Emby you point the cache, metedata, and transcode options to /mnt/share3 thereby moving that option away from your system drive. Hope that makes sense, I have done this previously and it works.