SnapRaid and mergerfs are different things and do not interoperate with each other. So if you aren't using mergerfs you don't need to pay attention to suggestions about its use.
Some programs that can be run in dockers have /config container side directories that will cause a lot of grief for SnapRaid unless they are excluded. One example is Plex's /config. Another is Smokeping. And there are many more. Rather than discover these one by one and exclude them one by one, I found it easier to put these all in one folder, confined to one drive, and exclude that folder. This leaves them all unprotected by SnapRaid, but I can live with that.
So for instance, my appdata currently resides in /srv/dev-disk-by-uuid-1d060b23-6aec-4855-85e7-c0cb380c0d19/appdata. I need to exclude that folder in /etc/snapraid.conf and also directly reference the full path when I am configuring a container (ie: no symlinks).