I have tried that with a share out of the mergerfs mountpoint, but with the same result. Restart after 4 seconds
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.
Raid is not a backup! Would you go skydiving without a parachute?