SQL Clone Agent Cert

If we set up the SQL Clone application to use a CA created cert, will that cert be carried over to the Agent that we install?  Currently, when an Agent is installed it appears to use a self-signed cert and our vulnerabilities team is tagging that as a vulnerability that needs to be resolved before we go to production.  I'm not an expert in all things certs, so any guidance would be appreciated.

Thoughts?
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