If I understand it correctly, the customer is registering Cluster (using custom user account) and not explicitly registering the individual SVMs. Modifying the cluster credentials from admin user to custom user account in SC UI is resulting in the error as reported.
There shouldn't be an issue using custom accounts with SnapCenter. The error "Failed to connect to the storage system" is usually given at times when SC is not able to reach the storage system specified. It can be even HTTPs timeout also.
If the network side seems to be fine, I would suggest the customer open a support ticket so that the concerned team can take a look at the logs for proper triage.