I'd reported a bug here
NAS-105995 which has now been fixed (thanks!) so I was able to disable my legacy replication task and create a new one to replicate my /mnt/pool/iocage dataset from one FreeNAS machine to another (both running 11.3-U3.1)
The replication task is showing success, but not all of the folders inside the dataset are being replicated, specifically, the jail one which is obviously the most important in terms of backing up my jails).
Am I missing something in the settings or is this a bug?