The operator makes it more flexible in terms of your options for restore, ie restoring rancher into a completely new cluster. Transplanting etcd between different clusters is not really viable. The backup operator is still just backing up custom resources that effectively make up your Rancher config.
It also helps in environments you don't have full control over etcd, such as hosted providers like EKS, AKS, GKE. It's also used as a migration tool to relocate Rancher if required.