Currently, dbRepository and javaDbRepository cannot be configured in Harbor and the alternative it is to have a runner regularly execute the following commands on the Trivy pods:

trivy image --download-db-only --db-repository registry.example.com/aquasecurity/trivy-db
trivy image --download-java-db-only --java-db-repository registry.example.com/aquasecurity/trivy-java-db

I probably should mention that the official Trivy helm chart does have a configurable dbRepository but not javaDbRepository (which has been added with trivy#3595).