If you are rotating an intermediate CA, there is a common root in both the new and the old CA chains and both are/will be provided to Vault, you do not need this option. You can manually replace the CA and use the regular kafka_certs option on the tool without risking downtime.
However, if you are rotating a root CA or have not/will not include the full chain on an intermediate CA, you should use the kafka_ca option as follows:
kubectl exec -it -n tm-system vault-installer -- /deployment-tools/rotate-certs
This may require user action in response to the prompts from the tool. It is designed to prevent downtime during the CA migration. If you are using Vault-installed Kafka, it will rotate the broker certificates for you, if not, you will be prompted to rotate the broker certificates manually.