This might be an "old" thread, but I have the exact same problem as the original poster. Adding or removing a path of an existing folder via the mergerfs ui in OMV 5.4 doesn't update my /etc/fstab file. Hence my /etc/fstab and the displayed configuration differ. But I found (after way too much trail and error) a work-around. By adding in the mergerfs ui a new folder with any path (I mostly use /mnt/ because it's empty) and then applying the configuration's change, the /etc/fstab is in fact updated. I then remove the newly added folder again, apply the configuration's change a second time and then everything in the /etc/fstab is as it should be according to the configuration in OMV.